Journal of Chemical Physics最新文献_第2页

A compartmentalized model of multiphase chemical kinetics. 多相化学动力学的分区模型。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0266383

Alexander M Prophet, Kevin R Wilson

引用次数: 0

EOM-CCSD calculation of metal K pre-edge spectra: 3d transition metal tetrachlorides. 金属K预边缘光谱的EOM-CCSD计算：三维过渡金属四氯化物。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0274777

Young Choon Park, Ajith Perera, Hyunsik Kim, Rodney J Bartlett

引用次数: 0

Binder and monomer valencies determine the extent of collapse and reswelling of chromatin. 结合剂和单体的价决定了染色质坍塌和溶胀的程度。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0236102

Sougata Guha

{"title":"Binder and monomer valencies determine the extent of collapse and reswelling of chromatin.","authors":"Sougata Guha","doi":"10.1063/5.0236102","DOIUrl":"https://doi.org/10.1063/5.0236102","url":null,"abstract":"Multivalent DNA-bridging protein-mediated collapse of chromatin polymers have long been established as one of the driving factors in chromatin organization inside cells. These multivalent proteins can bind to distant binding sites along the chromatin backbone and bring them together in spatial proximity, leading to collapsed conformations. Recently, it has been suggested that these proteins not only drive the collapse of the chromatin polymer but also reswelling at higher concentrations. In this study, we investigate the physical mechanisms underlying this unexpected reswelling behavior. We use the Langevin dynamics simulation of a coarse-grained homopolymer to investigate the effects of the valencies of both the binders and the monomers on the polymer conformations. We find that while the extent of collapse of the polymer is strongly dependent on the binder valency, the extent of reswelling is largely determined by the monomer valency. Furthermore, we also discovered two different physical mechanisms that drive the reswelling of the polymer-excluded volume effects and loss of long-range loops. Finally, we obtain a classification map to determine the regimes in which each of these mechanisms is the dominant factor leading to polymer reswelling.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Internal friction and energy dissipation during fracture in silicate glasses. 硅酸盐玻璃断裂过程中的内摩擦与能量耗散。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0255432

Tina Waurischk, Joachim Deubener, Ralf Müller

引用次数: 0

Understanding pathway complexity in assembly mechanisms of hydrophobic peptides in water: Insights from atomistic simulations via event tracking. 了解疏水肽在水中组装机制的途径复杂性：通过事件跟踪从原子模拟中获得的见解。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0261115

Argha Chakraborty, Rumela Adhikary, Sangeeta Das, Avisek Das

{"title":"Understanding pathway complexity in assembly mechanisms of hydrophobic peptides in water: Insights from atomistic simulations via event tracking.","authors":"Argha Chakraborty, Rumela Adhikary, Sangeeta Das, Avisek Das","doi":"10.1063/5.0261115","DOIUrl":"https://doi.org/10.1063/5.0261115","url":null,"abstract":"Complex pathways in spontaneous molecular assemblies have been envisaged to be crucial factors in determining diverse outcomes desirable for materials design. Computer simulations can be instrumental in elucidating early stages of the assembly process, where direct experimental observations are difficult to obtain. In this paper, we report a computational study on the pathway complexities in aqueous mixtures of hydrophobic tripeptides that self-assemble into amorphous nanoscale objects. We introduce a new algorithmic approach for \"complete accounting\" of the simulation data in terms of rearrangements of spatial clusters spanning multiple length and time scales without relying on a priori assumptions. The salient features of an assembly mechanism were analyzed by focusing on four types of \"events\" encompassing all possible redistribution of molecules among interacting clusters. The event tracking analysis of the dynamics of spontaneous assemblies observed in fully atomistic molecular dynamics trajectories of tri-phenylalanine, tri-leucine, and tri-isoleucine revealed non-classical pathways with a clear trend in terms of spatio-temporal hierarchy. The discernible differences between latter two systems, where the building blocks are constitutional isomers, were particularly striking. Tri-phenylalanine assembled by a strongly hierarchical mechanism involving fusions of clusters of varying sizes. On the other hand, tri-isoleucine mostly followed a ripening type growth process, where isolated molecules or small molecular clusters attached to a single growing cluster. The tri-leucine exhibited an intermediate behavior with subtle differences from other two systems. These results underscored the effectiveness of our new analysis protocol in deciphering pathway complexities in molecular assemblies hitherto unreported in the literature.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanism of nitrous oxide (HONO) formation in D-layer of ionosphere. 电离层d层氧化亚氮（HONO）形成机理。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0271255

Hiroto Tachikawa

引用次数: 0

Heterostructure engineering for wurtzite LaN. 纤锌矿局域网异质结构工程。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-21 DOI: 10.1063/5.0255815

A J E Rowberg, S Mu, C G Van de Walle

引用次数: 0

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF? 为什么组蛋白单甲基化和二甲基化会导致与LEDGF结合的显著差异？

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0259337

Hinako X Suzuki, Hisashi Okumura, Satoru G Itoh

引用次数: 0

Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results. 用超快电子衍射成像环丁酮的光化学：实验结果。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0266559

A E Green, Y Liu, F Allum, M Graßl, P Lenzen, M N R Ashfold, S Bhattacharyya, X Cheng, M Centurion, S W Crane, R Forbes, N A Goff, L Huang, B Kaufman, M-F Kling, P L Kramer, H V S Lam, K A Larsen, R Lemons, M-F Lin, A J Orr-Ewing, D Rolles, A Rudenko, S K Saha, J Searles, X Shen, S Weathersby, P M Weber, H Zhao, T J A Wolf

{"title":"Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results.","authors":"A E Green, Y Liu, F Allum, M Graßl, P Lenzen, M N R Ashfold, S Bhattacharyya, X Cheng, M Centurion, S W Crane, R Forbes, N A Goff, L Huang, B Kaufman, M-F Kling, P L Kramer, H V S Lam, K A Larsen, R Lemons, M-F Lin, A J Orr-Ewing, D Rolles, A Rudenko, S K Saha, J Searles, X Shen, S Weathersby, P M Weber, H Zhao, T J A Wolf","doi":"10.1063/5.0266559","DOIUrl":"https://doi.org/10.1063/5.0266559","url":null,"abstract":"We investigated the ultrafast structural dynamics of cyclobutanone following photoexcitation at λ = 200 nm using gas-phase megaelectronvolt ultrafast electron diffraction. Our investigation complements the simulation studies of the same process within this special issue. It provides information about both electronic state population and structural dynamics through well-separable inelastic and elastic electron scattering signatures. We observe the depopulation of the photoexcited S2 state of cyclobutanone with n3s Rydberg character through its inelastic electron scattering signature with a time constant of (0.29 ± 0.2) ps toward the S1 state. The S1 state population undergoes ring-opening via a Norrish Type-I reaction, likely while passing through a conical intersection with S0. The corresponding structural changes can be tracked by elastic electron scattering signatures. These changes appear with a delay of (0.14 ± 0.05) ps with respect to the initial photoexcitation, which is less than the S2 depopulation time constant. This behavior provides evidence for the ballistic nature of the ring-opening once the S1 state is reached. The resulting biradical species react further within (1.2 ± 0.2) ps via two rival fragmentation channels yielding ketene and ethylene, or propene and carbon monoxide. Our study showcases the value of both gas-phase ultrafast diffraction studies as an experimental benchmark for nonadiabatic dynamics simulation methods and the limits in the interpretation of such experimental data without comparison with such simulations.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods. apoCHARMM：基于gpu的高性能分子动力学模拟，用于高级模拟方法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0264937

Samarjeet Prasad, Felix Aviat, James E Gonzales, Bernard R Brooks

{"title":"apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.","authors":"Samarjeet Prasad, Felix Aviat, James E Gonzales, Bernard R Brooks","doi":"10.1063/5.0264937","DOIUrl":"10.1063/5.0264937","url":null,"abstract":"We present apoCHARMM, a high-performance molecular dynamics (MD) engine optimized for graphics processing unit (GPU) architectures, designed to accelerate the simulation of complex molecular systems. The distinctive features of apoCHARMM include single-GPU support for multiple Hamiltonians, computation of a full virial tensor for each Hamiltonian, and full support for orthorhombic periodic systems in both P1 and P21 space groups. Multiple Hamiltonians on a single GPU permit rapid single-GPU multi-dimensional replica exchange methods, multi-state enveloping distribution sampling methods, and several efficient free energy methods where efficiency is gained by eliminating post-processing requirements. The combination of these capabilities enables constant-pH molecular dynamics in explicit solvent with enveloping distribution sampling, where Hamiltonian replica exchange can be performed on a single GPU with minimal host-GPU memory transfers. A full atomic virial tensor allows support for many different pressure, surface tension, and temperature ensembles. Support for orthorhombic P21 systems allows for the simulation of lipid bilayers, where the two leaflets have equalized chemical potentials. apoCHARMM uses CUDA and modern C++ to enable efficient computation of energy, force, restraint, constraint, and integration calculations directly on the GPU. This GPU-exclusive design focus minimizes host-GPU memory transfers, ensuring optimal performance during simulations, with such transfers occurring only during logging or trajectory saving. Benchmark tests demonstrate that apoCHARMM achieves competitive or superior performance when compared to other GPU-based MD engines, positioning it as a versatile and useful tool for the molecular dynamics community.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12074570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0