The Journal of Chemical Physics
Articles in this Issue
A bilinear model for the elastic response of hydrated lipid bilayers under normal pressure difference
The elasticity of phospholipid membranes as a function of hydration was investigated using coarse-grained molecular simulations. Multilamellar membranes consist of two or more lipid bilayers separated...
Unraveling cation–cation “attraction” in argentophilic interaction in 2,2′-bipydine coordinated silver complex
The nature of argentophilic interaction in the 2,2′-bipyridine-coordinated silver complex, which manifests counterintuitive cation–cation “attraction,” is attributed to ligand stacking and solvation e...
Boron-based B3Zn6− alloy cluster as a hybrid between prismatic and sandwich-like structures: Stabilization of a linear B3 chain motif using electronic transmutation
Doping boron clusters with metallic elements can tune the structural, electronic, and bonding properties. We report on the computational design of a zinc-rich D3h (1A1′) B3Zn6− alloy cluster, whose gl...
Active polymer behavior in two dimensions: A comparative analysis of tangential and push–pull models
In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push–pull models, including a variant with passive end monomers, to bridge the t...
Modeling entanglement dynamics of molecules interacting with entangled photons through Lindblad master equation approach
This work presents a new approach for simulating the interaction between molecular aggregate systems and multi-modal energy–time entangled light by solving the Lindblad master equation. The density ma...
An <i>ab initio</i> deep neural network potential to study the effect of density on the thermal decomposition mechanism of FOX-7
Condensed phase explosives typically contain defects such as voids, bubbles, and pores; this heterogeneity facilitates the formation of hot spots and triggers decomposition reaction at low densities....
Local hybrid alternatives to the orbital density approximation reduce the orbital dependence of self-interaction corrected DFT and the overbinding of DFT-corrected correlated wavefunctions
This work presents local hybrid alternatives to the orbital density approximation employed in self-interaction corrected density functional theory (SIC-DFT) and extended for use in DFT-corrected corre...
Coherent nonlinear optical response for high-intensity excitation
The calculation of the coherent nonlinear response of a system is essential to correctly interpret results from advanced techniques such as two-dimensional coherent spectroscopy. Usually, even for the...
Toward a Monte Carlo simulation of protein systems in amino-acid sequence space
In this article, we present our strategy for studying amino-acid sequence dependences on protein structures. For this purpose, performing Metropolis Monte Carlo simulations in the amino-acid sequence...
Revisiting the question of what instantaneous normal modes tell us about liquid dynamics
The lack of a well-defined equilibrium reference configuration has long hindered a comprehensive atomic-level understanding of liquid dynamics and properties. The Instantaneous Normal Mode (INM) appro...
The structure and symmetry of modular state space for complex quantum systems
Understanding the state space structure of complex quantum systems can help to effectively characterize the system properties and explore underlying mechanisms. The structure of the state space could...
Time-frequency analysis of femtosecond CARS spectroscopy of N2 and O2 using the superlet transform
Molecular dynamics plays a crucial role in understanding molecular interactions, rovibrational coupling mechanisms, and energy transfer processes. Femtosecond time-resolved coherent anti-Stokes Raman...
Reaction-limited evaporation for the color-gradient lattice Boltzmann model
We propose a reaction-limited evaporation model within the color-gradient lattice Boltzmann (LB) multicomponent framework to address the lack of intrinsic evaporation mechanisms. Unlike diffusion-driv...
On the applicability of CCSD(T) for dispersion interactions in large conjugated systems
In light of the recent discrepancies reported between fixed node diffusion Monte Carlo and local natural orbital coupled cluster with single, double, and perturbative triples [CCSD(T)] methodologies f...
Erratum: “Alignment of ND3 molecules in dc-electric fields” [J. Chem. Phys. 160, 204305 (2024)]
Phase behavior of x-shaped liquid crystalline macromolecules
X-shaped liquid crystalline macromolecules (XLCMs) are obtained by tethering two flexible end A-blocks and two flexible side B-blocks to a semiflexible R-block. A rich array of ordered structures can...
Non-perturbative exciton transfer rate analysis of the Fenna–Matthews–Olson photosynthetic complex under reducing and oxidizing conditions
Two-dimensional optical spectroscopy experiments have examined photoprotective mechanisms in the Fenna–Matthews–Olson (FMO) photosynthetic complex, showing that exciton transfer pathways change signif...
How accurate are lattice models with Gaussian energy disorder in describing charge-carrier transport and reactions in amorphous organic semiconductors?
We model charge-carrier hopping transport and electron–hole recombination in realistic amorphous structures of different densities and use the obtained results to assess the quality of the lattice mod...
Protein solvation: Site-specific hydrophilicity, hydrophobicity, counter ions, and interaction entropy
Solvation free energy is a driving force that plays an important role in the stability of biomolecular conformations. Currently, the implicit solvent model is widely used to calculate solvation energi...
Strong coupling non-Markovian quantum thermodynamics of a finite-bath system
The focus is on understanding the quantum thermodynamics of strongly coupled non-Markovian quantum systems. To this end, a non-trivial, non-Markovian model of a central spin surrounded by a spin bath...
Spin migration in density functional theory: Energy, potential, and density perspectives
Spin is a fundamental property of any many-electron system. The ability of density functional theory to accurately predict the physical properties of a system, while varying its spin, is crucial for d...
Exploration of deep operator networks for predicting the piezoionic effect
The piezoionic effect holds significant promise for revolutionizing biomedical electronics and ionic skins. However, modeling this multiphysics phenomenon remains challenging due to its high complexit...
Local structural dynamics and vibrational energy transfer in an angiotensin receptor-neprilysin inhibitor by ultrafast 2D IR spectroscopy
As a novel drug-drug cocrystal, sacubitril allisartan calcium (S086) has demonstrated significant efficacy in the treatment of hypertension and heart failure. S086 has two crystalline forms (α and ξ)...
Adaptive kink filtration: Achieving asymptotic size-independence of path integral simulations utilizing the locality of interactions
Recent method developments involving path integral simulations have come a long way in making these techniques practical for studying condensed phase non-equilibrium phenomena. One of the main difficu...
Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces
The localization of biomolecular condensates to intracellular membrane surfaces has emerged as an important feature of sub-cellular organization. In this work, we study the wetting behavior of biomole...