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In this work, we introduce a novel approach for predicting thermodynamic properties of binary mixtures, which we call the similarity-based method (SBM). The method is based on quantifying the pairwise similarity of components, which we…

Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…

Microorganisms have developed complex regulatory features controlling their reaction and internal adaptation to changing environments. When modeling these organisms we usually do not have full understanding of the regulation and rely on…

Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…

Determining light shift in Raman-Ramsey interference is important for the development of atomic frequency standards based on a vapor cell. We have accurately calculated light shift in Raman-Ramsey interference using the density-matrix…

We recently introduced a mM-MCMC scheme that is able to accelerate the sampling of Gibbs distributions when there is a time-scale separation between the complete molecular dynamics and the slow dynamics of a low dimensional reaction…

Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…

Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modelling meticulously executed. Furthermore, to enable the…

Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…

Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…

Activity coefficients, which are a measure of the non-ideality of liquid mixtures, are a key property in chemical engineering with relevance to modeling chemical and phase equilibria as well as transport processes. Although experimental…

Alzheimer's Disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (ABeta) antibodies are the leading drug candidates to treat AD, but the results of clinical trials have been disappointing.…

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…

Systematic calculations of the Coulomb barrier parameters for collisions of spherical nuclei are performed within the framework of the double folding approach. The value of the parameter $B_Z=Z_PZ_T/(A^{1/3}_P+(A^{1/3}_P)$ (which estimates…

In this paper, a new Computation-Control Motion Estimation (CCME) method is proposed which can perform Motion Estimation (ME) adaptively under different computation or power budgets while keeping high coding performance. We first propose a…

Approximate Bayesian Computation is widely used to infer the parameters of discrete-state continuous-time Markov networks. In this work, we focus on models that are governed by the Chemical Master Equation (the CME). Whilst originally…

Many proteins undergo conformational changes during their activity. A full understanding of the function of these proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution,…

Stochastic systems in biology often exhibit substantial variability within and between cells. This variability, as well as having dramatic functional consequences, provides information about the underlying details of the system's behaviour.…

We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…

Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…