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RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
The adsorption or adhesion of large particles (proteins, colloids, cells, >...) at the liquid-solid interface plays an important role in many diverse applications. Despite the apparent complexity of the process, two features are…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Metamorphic proteins like Lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three dimensional structure. In particular, the human chemokine lymphotactin protein (Ltn) exists in…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
The adsorption at the interface between an aqueous solution of several surface-active agents and another fluid (air or oil) phase is addressed theoretically. We derive the kinetic equations from a variation of the interfacial free energy,…
The diffuse-interface model for two-phase flows with soluble surfactants has garnered considerable attention due to its ability to circumvent the need for Robin boundary condition in the bulk surfactant transport equation. However, the…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a…
Transient absorption in plasmonic materials has recently attracted attention of the chemistry and optics communities as a technique to understand dynamic processes and hot carriers generation on ultrafast timescales. In this context, hybrid…
Applications like high density information storage, neuromorphic computing, nanophotonics, etc. require ultra-thin electronic devices which can be controlled with applied electric field. Of late, atomically thin two-dimensional (2D)…
RNA polymerase (RNAP) elongates RNA by walking along a DNA template and selectively incorporating ribonucleoside triphosphates (rNTPs). Rather than mechanically replicating the base sequence, RNAP conditions binding and chemistry on the…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
We study the vicinal surface of the restricted solid-on-solid model coupled with the Langmuir adsorbates which we regard as two-dimensional lattice gas without lateral interaction. The effect of the vapor pressure of the adsorbates in the…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting…