Tạp chí Khoa học Trường Đại học Cần Thơ, Apr 29, 2022
Công tác quản lý nhà nước, khung pháp lý, xâm nhập mặn và tài nguyên nước Từ khóa: Công tác quản ... more Công tác quản lý nhà nước, khung pháp lý, xâm nhập mặn và tài nguyên nước Từ khóa: Công tác quản lý nhà nước, khung pháp lý, xâm nhập mặn và tài nguyên nước
The transition to multicore processors has brought synchronization, a fundamental challenge in co... more The transition to multicore processors has brought synchronization, a fundamental challenge in computer science, into focus. In looking for solutions to the problem, interest has developed in the lock-free approach, which has been proven to achieve several advantages over the traditional mutual exclusion approach. This thesis studies challenges in interprocess synchronization in shared memory multicore systems using the lock-free approach. Our contributions focus on efficient design and implementation, composition, and dynamic memory reclamation of lock-free data structures, a key component in lock-free solutions to synchronization problems. First, we show that lock-free synchronization offers several advantages. Lock-free implementations of data structures can achieve decent throughput performance while managing to provide competitive fairness among the sharing participants in accessing the shared data. We also show that although lockfreedom does not guarantee starvation-freedom, it is composable in terms of the progress guarantee. Multiple lock-free data objects can concurrently use another lock-free object without compromising their lock-free progress guarantees because operations they invoke at that object get starved. Having shown that lock-free synchronization possesses several advantages, we then propose lock-free implementations of data structures, as they play a vital role in solving synchronization problems. We present a lock-free hash table based on cuckoo hashing scheme and a lock-free skip-list with extended functionality. Cuckoo hashing uses two hash tables to offer two positions for any key, so hashing conflicts are solved efficiently and simply by placing conflicted keys in different positions. We develop a lock-free implementation by addressing challenges in manipulating elements in their two possible positions. The evaluation results show that our lock-free cuckoo hash table outperforms other I am honored to have Michael Spear from Lehigh University as my opponent. I would like to thank Marina Papatriantafilou for her support and many helpful insights for my research. I thank Thierry Coquand-my examiner, Patrik Jansson and Gerardo Schneider for their constructive discussions during my follow-up meetings. I also would like to thank Håkan Sundell from Borås University, and Marc Shapiro, Lokesh Gidra, Gäel Thomas, and Julien Sopena from LIP6, Université Pierre et Marie Curie for their collaboration. I thank my two cool office mates, Zhang and Bapi, for fun times and for a lot of interesting discussions. I want to give my appreciation to Daniel and Yiannis from Distributed Computing and Systems group for their support and collaboration. I thank the rest of the colleagues in the group: Giorgos, Andreas,
This brief announcement provides a high level overview of a parallel mark-split garbage collector... more This brief announcement provides a high level overview of a parallel mark-split garbage collector. Our parallel design introduces and makes use of an efficient concurrency control mechanism based on a lock-free skip-list design for handling the list of free memory intervals. We have implemented the parallel mark-split garbage collector in OpenJDK HotSpot as a parallel and concurrent garbage collector for the old generation. We experimentally evaluate the collector and compare it with the default concurrent mark-sweep garbage collector in OpenJDK HotSpot, using the DaCapo benchmarks.
A comprehensive effort to examine the real-time, molecular-level response of shock compressed cyc... more A comprehensive effort to examine the real-time, molecular-level response of shock compressed cyclotrimethylene trinitramine (RDX) single crystals, using Raman and emission spectroscopy, is summarized. Single crystals of [111], [210], or [100] orientation were shocked under stepwise loading to peak stresses from 3 to 20 GPa. The shock experiments were complemented by static high pressure measurements and quantum chemical calculations. This work has provided evidence for structural phase transition in shocked RDX; examined the anisotropic response below and above the stress threshold for decomposition; and proposed decomposition pathways for shocked crystal
Highly concurrent and reliable data objects are vital for parallel programming. Lock-free shared ... more Highly concurrent and reliable data objects are vital for parallel programming. Lock-free shared data objects are highly concurrent and guarantee that at least one operation, from a set of concurrently executed operations, finishes after a finite number of steps regardless of the state of the other operations. Lock-free data objects provide progress guarantees on the object level. In this paper, we first examine the progress guarantees provided by lock-free shared data objects that have been constructed by composing other lock-free data objects. We observe that although lock-free data objects are composable when it comes to linearizability, when it comes to progress guarantees they are not. More specifically we show that when a lock-free data object is used as a component (is shared) by two or more lock-free data objects concurrently, these objects can no longer guarantee lock-free progress. This makes it impossible for programmers to directly compose lock-free data objects and guarantee lock-freedom. To help programmability in concurrent settings, this paper presents a new synchronization mechanism for composing lock-free data objects. The proposed synchronization mechanism provides an interface to be used when calling a lock-free object from other lock-free objects, and guarantees lock-free progress for every object constructed. An experimental evaluation of the performance cost that the new mechanism introduces, as expected, for providing progress guarantees is also presented.
The translational diffusion constant, D, of dioxygen has been measured in eleven n-alkanes, two b... more The translational diffusion constant, D, of dioxygen has been measured in eleven n-alkanes, two branched alkanes, four cyclohexane derivatives and cis-decalin and trans-decalin while the D values for biphenyl, pyrene, and rubrene have been measured in the n-alkanes. The D values were determined in solutions drawn through a microcapillary by reduced pressure and decrease as the solution viscosity increases. The
2014 IEEE 34th International Conference on Distributed Computing Systems, 2014
This paper presents a lock-free cuckoo hashing algorithm; to the best of our knowledge this is th... more This paper presents a lock-free cuckoo hashing algorithm; to the best of our knowledge this is the first lockfree cuckoo hashing in the literature. The algorithm allows mutating operations to operate concurrently with query ones and requires only single word compare-and-swap primitives. Query of items can operate concurrently with others mutating operations, thanks to the two-round query protocol enhanced with a logical clock technique. When an insertion triggers a sequence of key displacements, instead of locking the whole cuckoo path, our algorithm breaks down the chain of relocations into several single relocations which can be executed independently and concurrently with other operations. A fine tuned synchronization and a helping mechanism for relocation are designed. The mechanisms allow high concurrency and provide progress guarantees for the data structure's operations. Our experimental results show that our lock-free cuckoo hashing performs consistently better than two efficient lockbased hashing algorithms, the chained and the hopscotch hashmap, in different access pattern scenarios.
Squalene, an intermediate in the biosynthesis of cholesterol, has a 24-carbon backbone with six m... more Squalene, an intermediate in the biosynthesis of cholesterol, has a 24-carbon backbone with six methyl groups and six isolated double bonds. Capillary flow techniques have been used to determine its translational diffusion constant, D, at room temperature in squalane, n-C16, and three n-C8-squalane mixtures. The D values have a weaker dependence on viscosity, η, than predicted by the Stokes-Einstein relation, D = kBT/(6πηr). A fit to the modified relation, D/T = ASE/η(p), gives p = 0.820 ± 0.028; p = 1 for the Stokes-Einstein limit. The translational motion of squalene appears to be much like that of n-alkane solutes with comparable chain lengths; their D values show similar deviations from the Stokes-Einstein model. The n-alkane with the same carbon chain length as squalene, n-C24, has a near-equal p value of 0.844 ± 0.018 in n-alkane solvents. The values of the hydrodynamic radius, r, for n-C24, squalene, and other n-alkane solutes decrease as the viscosity increases and have a common dependence on the van der Waals volumes of the solute and solvent. The possibility of studying squalene in lipid droplets and membranes is discussed.
The CP43 core antenna complex of Photosystem II is known to possess two quasi-degenerate "red"-tr... more The CP43 core antenna complex of Photosystem II is known to possess two quasi-degenerate "red"-trap states [R.
The CP43 protein complex of the core antenna of higher plant photosystem II (PSII) has two quasid... more The CP43 protein complex of the core antenna of higher plant photosystem II (PSII) has two quasidegenerate "red" absorption states. It has been shown in the accompanying paper I (Dang, N. C., et al. J. Phys. Chem. B 2008, 112, 9921.) that the site distribution functions (SDFs) of red-states A and B are uncorrelated and the narrow holes are burned in subpopulations of chlorophylls (Chls) from states A and B that are the lowestenergy pigments in their particular CP43 complexes and cannot further transfer energy downhill. In this work, we present the results of a series of Monte Carlo simulations using the 3.0-Å structure of the PSII core complex from cyanobacteria (Loll, B., et al. Nature 2005, 303, 1040.) to model absorption, emission, persistent, and transient hole burned (HB) spectra. At the current structural resolution, we found calculated site energies (obtained from INDO/S calculations) to be only suggestive because their values are different for the two monomers of CP43 in the PS II dimer. As a result, to probe the excitonic structure, a simple fitting procedure was employed to optimize Chl site energies from various starting values corresponding to different A/B pigment combinations to provide simultaneously good fits to several types of optical spectra. It is demonstrated that the shape of the calculated absorption, emission, and transient/persistent hole-burned spectra is consistent with experimental data and our model for excitation energy transfer between two quasi-degenerate lowest-E states (A and B) with uncorrelated SDFs discussed in paper I. Calculations revealed that absorption changes observed near 670 nm in the non-line-narrowed persistent HB spectra (assigned to photoconversion involving Chl-protein hydrogen-bonding by Hughes (Biochemistry 2006, 45, 12345.) are most likely the result of nonphotochemical hole-burning (NPHB) accompanied by the redistribution of oscillator strength due to modified excitonic interactions. We argue that a unique redistribution of oscillator strength during the NPHB process helps to assign Chls contributing to the low-energy states. It is demonstrated that the 4.2 K asymmetric triplet-bottleneck (transient) hole is mostly contributed to by both A and B states, with the hole profile described by a subensemble of pigments, which are the lowest-energy pigments (B sand A s-type) in their complexes. The same lowest-energy Chls contribute to the observed fluorescence spectra. On the basis of our excitonic calculations, the best Chl candidates that contribute to the low-energy A and B states are Chl 44 and Chl 37, respectively.
Using hole-burning spectroscopy, we show that excitation energy transfer (EET) time in ethynyl-li... more Using hole-burning spectroscopy, we show that excitation energy transfer (EET) time in ethynyl-linked chlorophyll trefoil (ChlT1) monomer is very fast (∼2.5 ps) at liquid helium temperature. This is consistent with data obtained by femtosecond transient spectroscopy experiments performed at room temperature, in which an EET time of 1.8 ps was observed (Kelley, R. F. et al. Angew. Chem. Int. Ed. 2006, 45, 7979). This finding further supports the importance of through-bond electronic coupling at low temperature. In addition, we show that ChlT1 (even at very low concentrations) in methyl tetrahydrofuranÀethanol glass (1:200 v/v; T ∼ 5 K) forms different types of aggregates. It is demonstrated that the relative distribution of various types of aggregates (whose possible structures are briefly discussed) depends on the cooling rate and matrix composition. For example, the EET time in two types of ChlT1-based aggregates is slower by a factor of ∼5À7 with respect to that observed for ChlT1 monomer. This indicates that ChlT1 aggregates can retain ultrafast energy transfer properties similar to those observed in natural photosynthetic antennas. It is anticipated that such building blocks could be utilized in future photovoltaic devices.
The translational diffusion constants, D T , of the bis(maleonitriledithiolato)nickel anion and d... more The translational diffusion constants, D T , of the bis(maleonitriledithiolato)nickel anion and dianion, Ni(mnt) 2and Ni(mnt) 2 2-, respectively, have been measured in acetone and ethyl alcohol solutions drawn through a microcapillary by reduced pressure at 25°C. The translational radius, r t , obtained from D T is larger for Ni(mnt) 2 2than for Ni(mnt) 2-in both solvents. The larger r t for Ni(mnt) 2 2is attributed to ion pairing with (n-Bu) 4 N + , while Ni(mnt) 2-does not appear to be ion paired. r t for Ni(mnt) 2-has been used to determine the rotational radius, r o , of this paramagnetic ion; r o has been used with ESR results to determine κ ⊥ , the solvent interaction parameter for Ni(mnt) 2-in several solvents. ESR studies of Ni(mnt) 2-in dimethyl phthalate (DMPT) and tris(2-ethylhexyl) phosphate (TEHP) have also been made. The analysis of the widths shows the reorientation of Ni(mnt) 2-is fastest about its long in-plane axis by a factor of ≈3 in both solvents. The temperature dependence of the widths is discussed using the modified Stokes-Einstein-Debye (SED) model and the Vogel-Tammann-Fulcher (VTF) equation. The SED results indicate that Ni(mnt) 2-has relatively weak interactions with both DMPT and TEHP. The ESR VTF parameters are consistent with those from viscosities and produce calculated values of the glass transition temperatures, T g , that are also in general agreement with experiment.
The translational diffusion constant, D, of dioxygen, O 2 , has been measured in the odd n-alkane... more The translational diffusion constant, D, of dioxygen, O 2 , has been measured in the odd n-alkanes n-C 7 H 16 to n-C 15 H 32 , two branched alkanes (isooctane and squalane), and several cycloalkanes (cyclohexane, methylcyclohexane, n-butylcyclohexane, dicyclohexyl, cis-decalin, and trans-decalin). The D values were determined using Taylor-Aris dispersion theory in solutions drawn through a microcapillary by reduced pressure. The initial analysis of the data was in terms of the Stokes-Einstein relation (D) k B T/6πηr). In both the n-alkanes and cycloalkanes, the values of the hydrodynamic radius r for O 2 are smaller than its known dimensions and decrease as the viscosity η increases, i.e., O 2 is diffusing faster than predicted by a constant solute "size." The data can be fitted to D/T) A/η p with p < 1 (p) 1 for the Stokes-Einstein relation). When the data for the odd n-alkanes are combined with our earlier results for O 2 in the even n-alkanes (n-C 6 H 14 to n-C 16 H 34 , Kowert, B. A.; Dang, N. C. J. Phys. Chem. 1999, 103, 779), we find p) 0.553 (0.009. For O 2 in the cycloalkanes the fit gives p) 0.632 (0.017. The data for isooctane and squalane are in approximate agreement with the n-alkane fit. The D values are also discussed in terms of computer simulations for small penetrants in hydrocarbons, the molar volumes of the solvents, and free volume approaches. A correlation between the p values and results of the free volume analyses is noted and discussed.
... 27) Chandler, D. J. Chem. Phys. 1975, 62, 1358. ... Size-Dependent Diffusion in the n-Alkanes... more ... 27) Chandler, D. J. Chem. Phys. 1975, 62, 1358. ... Size-Dependent Diffusion in the n-Alkanes. Bruce A. Kowert, Kurtis T. Sobush, Chantel F. Fuqua, Courtney L. Mapes, Jared B. Jones, and Jacob A. Zahm. The Journal of Physical Chemistry A 2003 107 (24), 4790-4795. ...
The translational diffusion constants, D, of biphenyl, diphenylacetylene, diphenylbutadiyne, anth... more The translational diffusion constants, D, of biphenyl, diphenylacetylene, diphenylbutadiyne, anthracene, pyrene, rubrene, perylene, and coronene have been determined in the n-alkanes using capillary flow techniques. Pyrene and rubrene were also studied in cyclohexane and several of its derivatives. The solutes showed varying degrees of deviation from the Stokes−Einstein (SE) relation (D = kBT/6πηr); the values of the hydrodynamic radius r decrease as the viscosity η increases. The data can be fitted to D/T = A/ηp with p < 1 (p = 1 for the SE relation). The values of p increase as the solute size increases. In the n-alkanes, they range from p = 0.718 ± 0.004 for biphenyl to p = 0.943 ± 0.014 for rubrene; the largest value (p = 0.982 ± 0.019) is found for rubrene in the cyclohexanes. The D values have been compared with reorientational results and molecular dynamics calculations; they have also been fitted to the Doolittle−Cohen−Turnbull free volume equation. A correlation between the p values and the resul...
The translational diffusion constant, D, of C60 has been determined in the even n-alkanes n-C6H14... more The translational diffusion constant, D, of C60 has been determined in the even n-alkanes n-C6H14 to n-C16H34 using microcapillary techniques and Taylor-Aris dispersion theory. Experiments were conducted over extended periods of time to ensure that the solute was not associated with itself or with solvent. The D values show deviations from the Stokes−Einstein (SE) relation (D = kT/6πηr); the values of the solute's hydrodynamic radius r decrease as the solvent viscosity η increases. The data can be fitted to D/T = ASE/ηp with p = 0.903 ± 0.006 (p = 1 for the SE relation).
Plate impact experiments on the (210), (100), and (111) planes were performed to examine the role... more Plate impact experiments on the (210), (100), and (111) planes were performed to examine the role of crystalline anisotropy on the shock-induced decomposition of cyclotrimethylenetrinitramine (RDX) crystals. Time-resolved emission spectroscopy was used to probe the decomposition of single crystals shocked to peak stresses ranging between 7 and 20 GPa. Emission produced by decomposition intermediates was analyzed in terms of induction time to emission, emission intensity, and the emission spectra shapes as a function of stress and time. Utilizing these features, we found that the shock-induced decomposition of RDX crystals exhibits considerable anisotropy. Crystals shocked on the (210) and (100) planes were more sensitive to decomposition than crystals shocked on the (111) plane. The possible sources of the observed anisotropy are discussed with regard to the inelastic deformation mechanisms of shocked RDX. Our results suggest that, despite the anisotropy observed for shock initiation, decomposition pathways for all three orientations are similar.
Abstract. Transient absorption spectra from 390-890 nm of laser shocked RDX, PETN, sapphire, and ... more Abstract. Transient absorption spectra from 390-890 nm of laser shocked RDX, PETN, sapphire, and polyvinylnitrate (PVN) at sub-nanosecond time scales are reported. RDX shows a nearly linear increase in absorption with time after shock at-23 GPa. PETN is ...
Tạp chí Khoa học Trường Đại học Cần Thơ, Apr 29, 2022
Công tác quản lý nhà nước, khung pháp lý, xâm nhập mặn và tài nguyên nước Từ khóa: Công tác quản ... more Công tác quản lý nhà nước, khung pháp lý, xâm nhập mặn và tài nguyên nước Từ khóa: Công tác quản lý nhà nước, khung pháp lý, xâm nhập mặn và tài nguyên nước
The transition to multicore processors has brought synchronization, a fundamental challenge in co... more The transition to multicore processors has brought synchronization, a fundamental challenge in computer science, into focus. In looking for solutions to the problem, interest has developed in the lock-free approach, which has been proven to achieve several advantages over the traditional mutual exclusion approach. This thesis studies challenges in interprocess synchronization in shared memory multicore systems using the lock-free approach. Our contributions focus on efficient design and implementation, composition, and dynamic memory reclamation of lock-free data structures, a key component in lock-free solutions to synchronization problems. First, we show that lock-free synchronization offers several advantages. Lock-free implementations of data structures can achieve decent throughput performance while managing to provide competitive fairness among the sharing participants in accessing the shared data. We also show that although lockfreedom does not guarantee starvation-freedom, it is composable in terms of the progress guarantee. Multiple lock-free data objects can concurrently use another lock-free object without compromising their lock-free progress guarantees because operations they invoke at that object get starved. Having shown that lock-free synchronization possesses several advantages, we then propose lock-free implementations of data structures, as they play a vital role in solving synchronization problems. We present a lock-free hash table based on cuckoo hashing scheme and a lock-free skip-list with extended functionality. Cuckoo hashing uses two hash tables to offer two positions for any key, so hashing conflicts are solved efficiently and simply by placing conflicted keys in different positions. We develop a lock-free implementation by addressing challenges in manipulating elements in their two possible positions. The evaluation results show that our lock-free cuckoo hash table outperforms other I am honored to have Michael Spear from Lehigh University as my opponent. I would like to thank Marina Papatriantafilou for her support and many helpful insights for my research. I thank Thierry Coquand-my examiner, Patrik Jansson and Gerardo Schneider for their constructive discussions during my follow-up meetings. I also would like to thank Håkan Sundell from Borås University, and Marc Shapiro, Lokesh Gidra, Gäel Thomas, and Julien Sopena from LIP6, Université Pierre et Marie Curie for their collaboration. I thank my two cool office mates, Zhang and Bapi, for fun times and for a lot of interesting discussions. I want to give my appreciation to Daniel and Yiannis from Distributed Computing and Systems group for their support and collaboration. I thank the rest of the colleagues in the group: Giorgos, Andreas,
This brief announcement provides a high level overview of a parallel mark-split garbage collector... more This brief announcement provides a high level overview of a parallel mark-split garbage collector. Our parallel design introduces and makes use of an efficient concurrency control mechanism based on a lock-free skip-list design for handling the list of free memory intervals. We have implemented the parallel mark-split garbage collector in OpenJDK HotSpot as a parallel and concurrent garbage collector for the old generation. We experimentally evaluate the collector and compare it with the default concurrent mark-sweep garbage collector in OpenJDK HotSpot, using the DaCapo benchmarks.
A comprehensive effort to examine the real-time, molecular-level response of shock compressed cyc... more A comprehensive effort to examine the real-time, molecular-level response of shock compressed cyclotrimethylene trinitramine (RDX) single crystals, using Raman and emission spectroscopy, is summarized. Single crystals of [111], [210], or [100] orientation were shocked under stepwise loading to peak stresses from 3 to 20 GPa. The shock experiments were complemented by static high pressure measurements and quantum chemical calculations. This work has provided evidence for structural phase transition in shocked RDX; examined the anisotropic response below and above the stress threshold for decomposition; and proposed decomposition pathways for shocked crystal
Highly concurrent and reliable data objects are vital for parallel programming. Lock-free shared ... more Highly concurrent and reliable data objects are vital for parallel programming. Lock-free shared data objects are highly concurrent and guarantee that at least one operation, from a set of concurrently executed operations, finishes after a finite number of steps regardless of the state of the other operations. Lock-free data objects provide progress guarantees on the object level. In this paper, we first examine the progress guarantees provided by lock-free shared data objects that have been constructed by composing other lock-free data objects. We observe that although lock-free data objects are composable when it comes to linearizability, when it comes to progress guarantees they are not. More specifically we show that when a lock-free data object is used as a component (is shared) by two or more lock-free data objects concurrently, these objects can no longer guarantee lock-free progress. This makes it impossible for programmers to directly compose lock-free data objects and guarantee lock-freedom. To help programmability in concurrent settings, this paper presents a new synchronization mechanism for composing lock-free data objects. The proposed synchronization mechanism provides an interface to be used when calling a lock-free object from other lock-free objects, and guarantees lock-free progress for every object constructed. An experimental evaluation of the performance cost that the new mechanism introduces, as expected, for providing progress guarantees is also presented.
The translational diffusion constant, D, of dioxygen has been measured in eleven n-alkanes, two b... more The translational diffusion constant, D, of dioxygen has been measured in eleven n-alkanes, two branched alkanes, four cyclohexane derivatives and cis-decalin and trans-decalin while the D values for biphenyl, pyrene, and rubrene have been measured in the n-alkanes. The D values were determined in solutions drawn through a microcapillary by reduced pressure and decrease as the solution viscosity increases. The
2014 IEEE 34th International Conference on Distributed Computing Systems, 2014
This paper presents a lock-free cuckoo hashing algorithm; to the best of our knowledge this is th... more This paper presents a lock-free cuckoo hashing algorithm; to the best of our knowledge this is the first lockfree cuckoo hashing in the literature. The algorithm allows mutating operations to operate concurrently with query ones and requires only single word compare-and-swap primitives. Query of items can operate concurrently with others mutating operations, thanks to the two-round query protocol enhanced with a logical clock technique. When an insertion triggers a sequence of key displacements, instead of locking the whole cuckoo path, our algorithm breaks down the chain of relocations into several single relocations which can be executed independently and concurrently with other operations. A fine tuned synchronization and a helping mechanism for relocation are designed. The mechanisms allow high concurrency and provide progress guarantees for the data structure's operations. Our experimental results show that our lock-free cuckoo hashing performs consistently better than two efficient lockbased hashing algorithms, the chained and the hopscotch hashmap, in different access pattern scenarios.
Squalene, an intermediate in the biosynthesis of cholesterol, has a 24-carbon backbone with six m... more Squalene, an intermediate in the biosynthesis of cholesterol, has a 24-carbon backbone with six methyl groups and six isolated double bonds. Capillary flow techniques have been used to determine its translational diffusion constant, D, at room temperature in squalane, n-C16, and three n-C8-squalane mixtures. The D values have a weaker dependence on viscosity, η, than predicted by the Stokes-Einstein relation, D = kBT/(6πηr). A fit to the modified relation, D/T = ASE/η(p), gives p = 0.820 ± 0.028; p = 1 for the Stokes-Einstein limit. The translational motion of squalene appears to be much like that of n-alkane solutes with comparable chain lengths; their D values show similar deviations from the Stokes-Einstein model. The n-alkane with the same carbon chain length as squalene, n-C24, has a near-equal p value of 0.844 ± 0.018 in n-alkane solvents. The values of the hydrodynamic radius, r, for n-C24, squalene, and other n-alkane solutes decrease as the viscosity increases and have a common dependence on the van der Waals volumes of the solute and solvent. The possibility of studying squalene in lipid droplets and membranes is discussed.
The CP43 core antenna complex of Photosystem II is known to possess two quasi-degenerate "red"-tr... more The CP43 core antenna complex of Photosystem II is known to possess two quasi-degenerate "red"-trap states [R.
The CP43 protein complex of the core antenna of higher plant photosystem II (PSII) has two quasid... more The CP43 protein complex of the core antenna of higher plant photosystem II (PSII) has two quasidegenerate "red" absorption states. It has been shown in the accompanying paper I (Dang, N. C., et al. J. Phys. Chem. B 2008, 112, 9921.) that the site distribution functions (SDFs) of red-states A and B are uncorrelated and the narrow holes are burned in subpopulations of chlorophylls (Chls) from states A and B that are the lowestenergy pigments in their particular CP43 complexes and cannot further transfer energy downhill. In this work, we present the results of a series of Monte Carlo simulations using the 3.0-Å structure of the PSII core complex from cyanobacteria (Loll, B., et al. Nature 2005, 303, 1040.) to model absorption, emission, persistent, and transient hole burned (HB) spectra. At the current structural resolution, we found calculated site energies (obtained from INDO/S calculations) to be only suggestive because their values are different for the two monomers of CP43 in the PS II dimer. As a result, to probe the excitonic structure, a simple fitting procedure was employed to optimize Chl site energies from various starting values corresponding to different A/B pigment combinations to provide simultaneously good fits to several types of optical spectra. It is demonstrated that the shape of the calculated absorption, emission, and transient/persistent hole-burned spectra is consistent with experimental data and our model for excitation energy transfer between two quasi-degenerate lowest-E states (A and B) with uncorrelated SDFs discussed in paper I. Calculations revealed that absorption changes observed near 670 nm in the non-line-narrowed persistent HB spectra (assigned to photoconversion involving Chl-protein hydrogen-bonding by Hughes (Biochemistry 2006, 45, 12345.) are most likely the result of nonphotochemical hole-burning (NPHB) accompanied by the redistribution of oscillator strength due to modified excitonic interactions. We argue that a unique redistribution of oscillator strength during the NPHB process helps to assign Chls contributing to the low-energy states. It is demonstrated that the 4.2 K asymmetric triplet-bottleneck (transient) hole is mostly contributed to by both A and B states, with the hole profile described by a subensemble of pigments, which are the lowest-energy pigments (B sand A s-type) in their complexes. The same lowest-energy Chls contribute to the observed fluorescence spectra. On the basis of our excitonic calculations, the best Chl candidates that contribute to the low-energy A and B states are Chl 44 and Chl 37, respectively.
Using hole-burning spectroscopy, we show that excitation energy transfer (EET) time in ethynyl-li... more Using hole-burning spectroscopy, we show that excitation energy transfer (EET) time in ethynyl-linked chlorophyll trefoil (ChlT1) monomer is very fast (∼2.5 ps) at liquid helium temperature. This is consistent with data obtained by femtosecond transient spectroscopy experiments performed at room temperature, in which an EET time of 1.8 ps was observed (Kelley, R. F. et al. Angew. Chem. Int. Ed. 2006, 45, 7979). This finding further supports the importance of through-bond electronic coupling at low temperature. In addition, we show that ChlT1 (even at very low concentrations) in methyl tetrahydrofuranÀethanol glass (1:200 v/v; T ∼ 5 K) forms different types of aggregates. It is demonstrated that the relative distribution of various types of aggregates (whose possible structures are briefly discussed) depends on the cooling rate and matrix composition. For example, the EET time in two types of ChlT1-based aggregates is slower by a factor of ∼5À7 with respect to that observed for ChlT1 monomer. This indicates that ChlT1 aggregates can retain ultrafast energy transfer properties similar to those observed in natural photosynthetic antennas. It is anticipated that such building blocks could be utilized in future photovoltaic devices.
The translational diffusion constants, D T , of the bis(maleonitriledithiolato)nickel anion and d... more The translational diffusion constants, D T , of the bis(maleonitriledithiolato)nickel anion and dianion, Ni(mnt) 2and Ni(mnt) 2 2-, respectively, have been measured in acetone and ethyl alcohol solutions drawn through a microcapillary by reduced pressure at 25°C. The translational radius, r t , obtained from D T is larger for Ni(mnt) 2 2than for Ni(mnt) 2-in both solvents. The larger r t for Ni(mnt) 2 2is attributed to ion pairing with (n-Bu) 4 N + , while Ni(mnt) 2-does not appear to be ion paired. r t for Ni(mnt) 2-has been used to determine the rotational radius, r o , of this paramagnetic ion; r o has been used with ESR results to determine κ ⊥ , the solvent interaction parameter for Ni(mnt) 2-in several solvents. ESR studies of Ni(mnt) 2-in dimethyl phthalate (DMPT) and tris(2-ethylhexyl) phosphate (TEHP) have also been made. The analysis of the widths shows the reorientation of Ni(mnt) 2-is fastest about its long in-plane axis by a factor of ≈3 in both solvents. The temperature dependence of the widths is discussed using the modified Stokes-Einstein-Debye (SED) model and the Vogel-Tammann-Fulcher (VTF) equation. The SED results indicate that Ni(mnt) 2-has relatively weak interactions with both DMPT and TEHP. The ESR VTF parameters are consistent with those from viscosities and produce calculated values of the glass transition temperatures, T g , that are also in general agreement with experiment.
The translational diffusion constant, D, of dioxygen, O 2 , has been measured in the odd n-alkane... more The translational diffusion constant, D, of dioxygen, O 2 , has been measured in the odd n-alkanes n-C 7 H 16 to n-C 15 H 32 , two branched alkanes (isooctane and squalane), and several cycloalkanes (cyclohexane, methylcyclohexane, n-butylcyclohexane, dicyclohexyl, cis-decalin, and trans-decalin). The D values were determined using Taylor-Aris dispersion theory in solutions drawn through a microcapillary by reduced pressure. The initial analysis of the data was in terms of the Stokes-Einstein relation (D) k B T/6πηr). In both the n-alkanes and cycloalkanes, the values of the hydrodynamic radius r for O 2 are smaller than its known dimensions and decrease as the viscosity η increases, i.e., O 2 is diffusing faster than predicted by a constant solute "size." The data can be fitted to D/T) A/η p with p < 1 (p) 1 for the Stokes-Einstein relation). When the data for the odd n-alkanes are combined with our earlier results for O 2 in the even n-alkanes (n-C 6 H 14 to n-C 16 H 34 , Kowert, B. A.; Dang, N. C. J. Phys. Chem. 1999, 103, 779), we find p) 0.553 (0.009. For O 2 in the cycloalkanes the fit gives p) 0.632 (0.017. The data for isooctane and squalane are in approximate agreement with the n-alkane fit. The D values are also discussed in terms of computer simulations for small penetrants in hydrocarbons, the molar volumes of the solvents, and free volume approaches. A correlation between the p values and results of the free volume analyses is noted and discussed.
... 27) Chandler, D. J. Chem. Phys. 1975, 62, 1358. ... Size-Dependent Diffusion in the n-Alkanes... more ... 27) Chandler, D. J. Chem. Phys. 1975, 62, 1358. ... Size-Dependent Diffusion in the n-Alkanes. Bruce A. Kowert, Kurtis T. Sobush, Chantel F. Fuqua, Courtney L. Mapes, Jared B. Jones, and Jacob A. Zahm. The Journal of Physical Chemistry A 2003 107 (24), 4790-4795. ...
The translational diffusion constants, D, of biphenyl, diphenylacetylene, diphenylbutadiyne, anth... more The translational diffusion constants, D, of biphenyl, diphenylacetylene, diphenylbutadiyne, anthracene, pyrene, rubrene, perylene, and coronene have been determined in the n-alkanes using capillary flow techniques. Pyrene and rubrene were also studied in cyclohexane and several of its derivatives. The solutes showed varying degrees of deviation from the Stokes−Einstein (SE) relation (D = kBT/6πηr); the values of the hydrodynamic radius r decrease as the viscosity η increases. The data can be fitted to D/T = A/ηp with p < 1 (p = 1 for the SE relation). The values of p increase as the solute size increases. In the n-alkanes, they range from p = 0.718 ± 0.004 for biphenyl to p = 0.943 ± 0.014 for rubrene; the largest value (p = 0.982 ± 0.019) is found for rubrene in the cyclohexanes. The D values have been compared with reorientational results and molecular dynamics calculations; they have also been fitted to the Doolittle−Cohen−Turnbull free volume equation. A correlation between the p values and the resul...
The translational diffusion constant, D, of C60 has been determined in the even n-alkanes n-C6H14... more The translational diffusion constant, D, of C60 has been determined in the even n-alkanes n-C6H14 to n-C16H34 using microcapillary techniques and Taylor-Aris dispersion theory. Experiments were conducted over extended periods of time to ensure that the solute was not associated with itself or with solvent. The D values show deviations from the Stokes−Einstein (SE) relation (D = kT/6πηr); the values of the solute's hydrodynamic radius r decrease as the solvent viscosity η increases. The data can be fitted to D/T = ASE/ηp with p = 0.903 ± 0.006 (p = 1 for the SE relation).
Plate impact experiments on the (210), (100), and (111) planes were performed to examine the role... more Plate impact experiments on the (210), (100), and (111) planes were performed to examine the role of crystalline anisotropy on the shock-induced decomposition of cyclotrimethylenetrinitramine (RDX) crystals. Time-resolved emission spectroscopy was used to probe the decomposition of single crystals shocked to peak stresses ranging between 7 and 20 GPa. Emission produced by decomposition intermediates was analyzed in terms of induction time to emission, emission intensity, and the emission spectra shapes as a function of stress and time. Utilizing these features, we found that the shock-induced decomposition of RDX crystals exhibits considerable anisotropy. Crystals shocked on the (210) and (100) planes were more sensitive to decomposition than crystals shocked on the (111) plane. The possible sources of the observed anisotropy are discussed with regard to the inelastic deformation mechanisms of shocked RDX. Our results suggest that, despite the anisotropy observed for shock initiation, decomposition pathways for all three orientations are similar.
Abstract. Transient absorption spectra from 390-890 nm of laser shocked RDX, PETN, sapphire, and ... more Abstract. Transient absorption spectra from 390-890 nm of laser shocked RDX, PETN, sapphire, and polyvinylnitrate (PVN) at sub-nanosecond time scales are reported. RDX shows a nearly linear increase in absorption with time after shock at-23 GPa. PETN is ...
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