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We present a numerical study of 2D random-bond Potts ferromagnets. The model is studied both below and above the critical value $Q_c=4$ which discriminates between second and first-order transitions in the pure system. Two geometries are…
A high fidelity model is developed for an elastic string pendulum, one end of which is attached to a rigid body while the other end is attached to an inertially fixed reel mechanism which allows the unstretched length of the string to be…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
The dynamics of a self-propelled particle are typically hard-wired by its microscopic construction, limiting the range of behaviors accessible without redesigning the particle itself. Here we show that intramolecular nonreciprocity provides…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed…
Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation of molecules in confined systems such as water in reverse micelles, cyclodextrin cavities and nano-tubes. Here we introduce…
Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…
In this work, we demonstrate how physical principles -- such as symmetries, invariances, and conservation laws -- can be integrated into the dynamic mode decomposition (DMD). DMD is a widely-used data analysis technique that extracts…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…
Single molecular magnets (SMMs) and Metal-Organic Frameworks (MOFs) attract significant interest due to their potential in quantum information processing, scalable quantum computing, and extended lifetimes and coherence times. The limiting…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Constrained Motion Planning (CMP) aims to find a collision-free path between the given start and goal configurations on the kinematic constraint manifolds. These problems appear in various scenarios ranging from object manipulation to…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…