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Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Biomolecular electrostatics is key in protein function and the chemical processes affecting it. Implicit-solvent models via the Poisson-Boltzmann (PB) equation provide insights with less computational cost than atomistic models, making…
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…
The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
We present a novel scattering emulator utilizing the complex scaling method to enhance nuclear reaction analysis. This approach leverages a single set of reduced bases, allowing for efficient and simultaneous emulation across multiple…
We have demonstrated a prototypical hybrid classical and quantum computational workflow for the quantification of protein-ligand interactions. The workflow combines the Density Matrix Embedding Theory (DMET) embedding procedure with the…
Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
In this work, we introduce Variational Umbrella Seeding, a novel technique for computing nucleation barriers. This new method, a refinement of the original seeding approach, is far less sensitive to the choice of order parameter for…
We determine both barrier heights and prefactors for protein folding by applying constraints determined from experimental rate measurements to a Kramers theory for folding rate. The theoretical values are required to match the experimental…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
Bridging functionalities in periodic mesoporous organosilicas (PMOs) enable new functionalities for a wide range of applications. Bridge cleavage is frequently observed during anneals required to form porous structures, yet the mechanism of…
Chemical clock reactions are characterised by a relatively long induction period followed by a rapid `switchover' during which the concentration of a \emph{clock chemical} rises rapidly. In addition to their interest in chemistry education,…
Motion estimation is the most critical process in video coding systems. First of all, it has a definitive impact on the rate-distortion performance given by the video encoder. Secondly, it is the most computationally intensive process…