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Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Predicting the impact of single-point amino acid mutations on protein stability is essential for understanding disease mechanisms and advancing drug development. Protein stability, quantified by changes in Gibbs free energy ($\Delta\Delta…
Polymer blends consisting of two or more polymers are important for a wide variety of industries and processes, but, the precise mechanism of their thermomechanical behaviour is incompletely understood. In order to understand clearly, it is…
While the simplest inflationary models predict the primordial perturbations to be near scale-invariant, the primordial power spectrum (PPS) can exhibit oscillatory features in many physically well-motivated models. We search for hints of…
There exist severe limitations on the accuracy of low-temperature thermometry, which poses a major challenge for future quantum-technological applications. Low-temperature sensitivity might be manipulated by tailoring the interactions…
In this work, we have carried out a two-dimensional (2D) simulation of thermal instability (TI) in interstellar matter (ISM), considering it to be a weakly ionised inviscid plasma with radiation loss. We carry out the simulation using our…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the…
Aligning theoretical atomistic structural models of materials with available experimental data presents a significant challenge for disordered systems. The configurational space to navigate is vast, and faithful realizations require large…
Accurate temperature regulation is critical for amperometric DNA analysis to achieve high fidelity, reliability, and throughput. In this work, a 9x6 cell array of mixed-signal CMOS distributed temperature regulators for on-CMOS multi-modal…
The field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. Thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which…
This work builds on the previous introduction [1] of a coupled experimental-computational system devised to fully characterize the thermal behavior of complex 3D submicron electronic devices. The new system replaces the laser-based surface…
The investigation of temperature dependence of damping and period of vibrations of HTSC superconductive cylinder of Bi-Pb-Sr-Ca-Cu-O system suspended by a thin elastic thread and performing axial-torsional vibrations in a magnetic field at…
Interacting-Particle Reaction Dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enable a wide range of…
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
A Rayleigh B\'enard instability study using the energy conserving dissipative particle dynamics method is presented here for the first time. The simulation is performed on an ideal dissipative particle dynamics fluid in a three dimensional…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…