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Interfaces play a crucial role in determining the overall performance and functionality of electronic devices and systems. Driven by the data science, machine learning (ML) reveals excellent guidance for material selection and device…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
Pituitary gonadotropins play an essential and pivotal role in the control of human and animal reproduction within the hypothalamic-pituitary-gonadal (HPG) axis. The computational modeling of pituitary gonadotropin signaling encompasses…
Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly…
G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet…
Front-Form Hamiltonian dynamics provides a framework in which QCD's vacuum is simple and states are boost invariant. However, canonical expressions are divergent and must be regulated in order to establish well-defined eigenvalue problems.…
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,…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Active Brownian particles (ABPs) are termed out to be a successful way of modeling the moving microorganism on the substrate. In recent studies, it is shown that such organisms can sense the characteristics of the substrate. Motivated by…
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules.…
Establishing the structure-property relationship for grain boundaries (GBs) is critical for developing next generation functional materials, but has been severely hampered due to its extremely large configurational space. Atomistic…
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional…
Gaussian process (GP) regression is a powerful probabilistic modeling technique with built-in uncertainty quantification. When one has access to multiple correlated simulations (tasks), it is common to fit a multitask GP (MTGP) surrogate…
Protein-protein interactions (PPIs) play a crucial role in numerous biological processes. Developing methods that predict binding affinity changes under substitution mutations is fundamental for modelling and re-engineering biological…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Entrainment of movement to a periodic stimulus is a characteristic intelligent behaviour in humans and an important goal for adaptive robotics. We demonstrate a quadruped central pattern generator (CPG), consisting of modified Matsuoka…
Bacterial assemblies exhibit rich collective behaviors that control their biological functions, making them a relevant object of study from an active matter physics perspective. Dense bacterial suspensions self-organize into distinct…
Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein conformational functionality is often dominated by long-range…
Lipid membranes regulate the flow of materials and information between cells and their organelles. Further, lipid composition and morphology can play a key role in regulating a variety of biological processes. For example, viral uptake,…
With the increasing demand for personalized health monitoring, wearable sensors have gained attention in medical diagnostics and physiological tracking. Hydrogels, known for their mechanical properties and similarity to biological tissues,…