Related papers: Intrinsic Dynamics of Protein-Peptide Unbinding
Action-detected two-dimensional electronic spectroscopy (A-2DES) could potentially be a versatile chemical tool with applicability across a range of photophysical observables such as photocurrent, photoionization, or fluorescence. However,…
A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but…
We study a system of two-dimensional Bose gases trapped in minima of a deep one-dimensional optical lattice potential. Increasing the tunneling amplitude between adjacent gases drives a deconfinement transition to a phase where coherence is…
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilised sucrose exhibited steadily increasing absorption with…
Spiropyran is a prototype photoswitch that undergoes photoinduced ring-opening via C-O bond fission. The quantum yield for this photochemical reaction is low, with photophysical relaxation being the dominant process. Previous theoretical…
We employ Molecular Dynamics (MD) and Time-Dependent Density Functional Theory (TDDFT) to explore the fluorescence of Hydrogen-bonded dimer and trimer structures of Cyclic FF (Phe- Phe) molecules. We show that in some of these…
The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the…
Actomyosin networks operate far from equilibrium, yet detecting the onset of motor-driven irreversible dynamics remains challenging. Here, we embed near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) within reconstituted…
Photoinduced isomerization reactions, including ring-opening reactions, lie at the heart of many processes in nature. The mechanisms of such reactions are determined by a delicate interplay of coupled electronic and nuclear dynamics…
Time-resolved multi-terahertz (THz) spectroscopy is used to observe pump fluence-dependent dynamics in the optical conductivity of photoexcited tin selenide (SnSe) over an ultrabroadband spectral range of 0.5 - 11 THz at fluences from 0.1 -…
Ultrafast light pulses can modify the electronic properties of quantum materials by perturbing the underlying, intertwined degrees of freedom. In particular, iron-based superconductors exhibit a strong coupling among electronic nematic…
Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…
Recent advancements in ultrashort and intense X-ray sources have enabled the utilisation of resonant inelastic X-ray scattering (RIXS) as a probing technique for monitoring photoinduced dynamics in molecular systems. To account for dynamic…
Understanding the biophysical and biochemical properties of molecular nanocarriers under physiological conditions and with minimal interference is crucial for advancing nanomedicine, photopharmacology, drug delivery, nanotheranostics and…
Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select'…
In this article, we study the kinetics of reversible ligand binding to receptors on a spherical cell surface using a self-consistent stochastic theory. Binding, dissociation, diffusion and rebinding of ligands are incorporated into the…
We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex ($P_1$$P_2$). The joint distribution $P(\tau_1,\tau_2)$ of unbinding lifetimes $\tau_1$ and $\tau_2$ measurable in…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…