相关论文: Redox Entropy of Plastocyanin: Developing a Micros…

Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50…

The Markov entropy decomposition (MED) is a recently-proposed, cluster-based simulation method for finite temperature quantum systems with arbitrary geometry. In this paper, we detail numerical algorithms for performing the required steps…

We build a comprehensive methodology for the fast computation of entropy across both solid and liquid phases. The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is…

We present an approximate method for calculating the electrostatic free energy of concentrated protein solutions. Our method uses a cell model and accounts for both the coulomb energy and the entropic cost of Donnan salt partitioning. The…

We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite…

We assess the validity of "microscopic" approaches of glass-forming liquids based on the sole k nowledge of the static pair density correlations. To do so we apply them to a benchmark provided by two liquid models that share very similar…

According to excess-entropy scaling, dynamic properties of liquids like viscosity and diffusion coefficient are determined by the entropy. This link between dynamics and thermodynamics is increasingly studied and of interest also for…

A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the…

Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…

Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering…

Geophysical flow simulations using hyperbolic shallow water moment equations require an efficient discretization of a potentially large system of PDEs, the so-called moment system. This calls for tailored model order reduction techniques…

We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…

Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…

Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy -- even with the aid of machine learning…

We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of…

We performed molecular dynamics simulations to investigate the viscoelastic properties of aqueous protein solutions containing an antifreeze protein, a toxin protein, and bovine serum albumin. These simulations covered a temperature range…

Water scarcity is a reality in our world, and scenarios predicted by leading scientists in this area indicate that it will worsen in the next decades. However, new technologies based in low-cost seawater desalination can prevent the worst…

Solvation of ions is ubiquitous on our planet. Solvated ions have a profound effect on the behavior of ionic solutions, which is crucial in nature and technology. Experimentally, ions have been classified into "structure makers" or…

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M.…

Fluctuating entropy production is studied for a set of linearly coupled complex fields. The general result is applied to non-equilibrium fluctuating hydrodynamic equations for coarse-grained fields (density, temperature and velocity), in…