Related papers: Water hexamer: Self-consistent phonons versus reve…
Free energy differences $\Delta F:=F-F_{\text{prism}}$ are computed for several isomers of water hexamer relative to the "prism" isomer using the self-consistent phonons method. %$\Delta F:=F-F({prism})$ We consider the isotope effect…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
We present the spatial regime conversion method (SRCM), a novel hybrid modelling framework for simulating reaction-diffusion systems that adaptively combines stochastic discrete and deterministic continuum representations. Extending the…
In the context of compressed sensing (CS), both Subspace Pursuit (SP) and Compressive Sampling Matching Pursuit (CoSaMP) are very important iterative greedy recovery algorithms which could reduce the recovery complexity greatly comparing…
Numerical schemes used for the integration of complex flow simulations should provide accurate solutions for the long time integrations these flows require. To this end, the performance of various high-order accurate numerical schemes is…
Self-consistent field theory (SCFT) is one of the most widely-used framework in studying the equilibrium phase behaviors of inhomogenous polymers. For liquid crystalline polymeric systems, the main numerical challenges of solving SCFT…
Accurate description of the excess charge in water cluster anions is challenging for standard semi-local and (global) hybrid density functional approximations (DFAs). Using the recent unitary invariant implementation of the Perdew-Zunger…
The Sllod equations of motion enable modeling of homogeneous flow at the atomic scale, and are commonly used to predict fluid properties such as viscosity. However, few publicly available codes support such simulations, and those that do…
A kernel-based method (kernelized minimal distributed charge model - kMDCM) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges whose positions adapts to the molecular geometry. Using Gaussian…
In our previous work, we developed a CCSD(T)-level range-separated water force field that combines the power of physics-driven and machine learning models. However, it was found that expensive CCSD(T)/CBS calculations lead to limited number…
Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper we explore the…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support…
I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed…
For molecules and solids, we developed efficient MPI-parallel algorithms for evaluating the second-order exchange term with bare, statically screened, and dynamically screened interactions. We employ the resulting term in a fully…
We present a careful comparison of two model-free control algorithms, Evolution Strategies (ES) and Proximal Policy Optimization (PPO), with receding horizon model predictive control (MPC) for operating simulated, price responsive water…
Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…
We introduce the Subspace Power Method (SPM) for calculating the CP decomposition of low-rank real symmetric tensors. This algorithm calculates one new CP component at a time, alternating between applying the shifted symmetric higher-order…
We present a new development of the force-coupling method (FCM) to address the accurate simulation of a large number of interacting micro-swimmers. Our approach is based on the squirmer model, which we adapt to the FCM framework, resulting…
Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called Approximate Non-Conformal (ANC) and generalized…
1H spin-lattice relaxation experiments have been performed for water - Bovine Serum Al-bumin (BSA) mixtures including 20% wt and 40% wt of BSA. The experiments have been carried out in a frequency range encompassing three orders of…