Search Results - "The Journal of chemical physics"

Numerically "exact" approach to open quantum dynamics: The hierarchical equations of motion (HEOM) by Tanimura, Yoshitaka

“…An open quantum system refers to a system that is further coupled to a bath system consisting of surrounding radiation fields, atoms, molecules, or proteins…”
Get more information

Perspective: Coarse-grained models for biomolecular systems by Noid, W G

“…By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual…”
Get more information

The physics of active polymers and filaments by Winkler, Roland G, Gompper, Gerhard

“…Active matter agents consume internal energy or extract energy from the environment for locomotion and force generation. Already, rather generic models, such…”
Get more information

Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory by Klimeš, Jirí, Michaelides, Angelos

“…Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals, and many other systems…”
Get more information

Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states by Gur, Mert, Taka, Elhan, Yilmaz, Sema Zeynep, Kilinc, Ceren, Aktas, Umut, Golcuk, Mert

“…In 2020, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people worldwide and caused the coronavirus disease…”
Get more information

Perspective: Sloppiness and emergent theories in physics, biology, and beyond by Transtrum, Mark K, Machta, Benjamin B, Brown, Kevin S, Daniels, Bryan C, Myers, Christopher R, Sethna, James P

“…Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are…”
Get more information

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization by Duboué-Dijon, E, Javanainen, M, Delcroix, P, Jungwirth, P, Martinez-Seara, H

“…Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the…”
Get more information

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories by Melo, Marcelo C R, Bernardi, Rafael C, de la Fuente-Nunez, Cesar, Luthey-Schulten, Zaida

“…Molecular interactions are essential for regulation of cellular processes from the formation of multi-protein complexes to the allosteric activation of…”
Get more information

Markov models of molecular kinetics: generation and validation by Prinz, Jan-Hendrik, Wu, Hao, Sarich, Marco, Keller, Bettina, Senne, Martin, Held, Martin, Chodera, John D, Schütte, Christof, Noé, Frank

“…Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete…”
Get more information

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding by Wang, Jinan, Miao, Yinglong

“…Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is…”
Get more information

Perspective: Identification of collective variables and metastable states of protein dynamics by Sittel, Florian, Stock, Gerhard

“…The statistical analysis of molecular dynamics simulations requires dimensionality reduction techniques, which yield a low-dimensional set of collective…”
Get more information

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis by Warshel, Arieh, Bora, Ram Prasad

“…Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the…”
Get more information

Density-functional approaches to noncovalent interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals by Burns, Lori A, Vázquez-Mayagoitia, Alvaro, Sumpter, Bobby G, Sherrill, C David

“…A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is…”
Get more information

Perspective: Stochastic algorithms for chemical kinetics by Gillespie, Daniel T, Hellander, Andreas, Petzold, Linda R

“…We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute,…”
Get more information

Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism by Li, Zhen, Bian, Xin, Li, Xiantao, Karniadakis, George Em

“…The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated…”
Get more information

Real-time and imaginary-time quantum hierarchal Fokker-Planck equations by Tanimura, Yoshitaka

“…We consider a quantum mechanical system represented in phase space (referred to hereafter as "Wigner space"), coupled to a harmonic oscillator bath. We derive…”
Get more information

Phase separation vs aggregation behavior for model disordered proteins by Rana, Ushnish, Brangwynne, Clifford P, Panagiotopoulos, Athanassios Z

“…Liquid-liquid phase separation (LLPS) is widely utilized by the cell to organize and regulate various biochemical processes. Although the LLPS of proteins is…”
Get more information

Low rank factorization of the Coulomb integrals for periodic coupled cluster theory by Hummel, Felix, Tsatsoulis, Theodoros, Grüneis, Andreas

“…We study a tensor hypercontraction decomposition of the Coulomb integrals of periodic systems where the integrals are factorized into a contraction of six…”
Get more information

How fast does water flow in carbon nanotubes? by Kannam, Sridhar Kumar, Todd, B D, Hansen, J S, Daivis, Peter J

“…The purpose of this paper is threefold. First, we review the existing literature on flow rates of water in carbon nanotubes. Data for the slip length which…”
Get more information

The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol by Cignoni, Edoardo, Slama, Vladislav, Cupellini, Lorenzo, Mennucci, Benedetta

“…The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of…”
Get more information