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Model-driven analysis of biophysical phenomena is gaining increased attention and utility for medical imaging applications. In magnetic resonance imaging (MRI), the availability of well-established models for describing the relations…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
The dielectric constant, which defines the polarization of the media, is a key quantity in condensed matter. It determines several electronic and optoelectronic properties important for a plethora of modern technologies from computer memory…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Enhanced optical absorption of molecules in the vicinity of metallic nanostructures is key to a number of surface-enhanced spectroscopies and of great general interest to the fields of plasmonics and nano-optics. Yet, experimental access to…
The interaction of proteins with small molecules is fundamental to their function in living organisms and it is widely studied in drug development. Here we compare optical trapping dynamics of streptavidin and biotinylated streptavidin…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
Understanding the dynamical processes that govern the performance of functional materials is essential for the design of next generation materials to tackle global energy and environmental challenges. Many of these processes involve the…
The relationship between the microscopic arrangement of molecules in a supercooled liquid and its slow dynamics at low temperature near glass transition is studied by Molecular Dynamics (MD) simulations. A Lennard-Jones liquid with…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Photo-induced magnetic force between nanostructures, at optical frequencies, is investigated theoretically. Till now optical magnetic effects are not used in scanning probe microscopy because of the vanishing natural magnetism with…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
Industrial polymeric materials often rely on antioxidants to achieve long-term reliability. Previous studies have frequently discussed the stabilization effect in the presence of macroscopic additive migration. However, the micro- to…
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…