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Accurate atomistic biomolecular simulations are vital for disease mechanism understanding, drug discovery, and biomaterial design, but existing simulation methods exhibit significant limitations. Classical force fields are efficient but…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
Temporal analysis of products (TAP) reactors enable experiments that probe numerous kinetic processes within a single set of experimental data through variations in pulse intensity, delay, or temperature. Selecting additional TAP…
Imidazole and 1,2,3-triazole are promising hydrogen-bonded heterocycles that conduct protons via a structural mechanism and whose derivatives are present in systems ranging from biological proton channels to proton exchange membrane fuel…
In a mesoscopic system, under zero bias voltage, a finite charge is transferred by quantum adiabatic pumping by adiabatically and periodically changing two or more control parameters. We obtained expressions for the pumped charge for a ring…
Understanding and prediction of the chemical reactions are fundamental demanding in the study of many complex chemical systems. Reactive molecular dynamics (MD) simulation has been widely used for this purpose as it can offer atomic details…
F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in the mitochondrial membranes and bacterial inner membranes in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons…
Biomolecular light-harvesting antennas operate as nanoscale devices in a regime where the coherent interactions of individual light, matter and vibrational quanta are non-perturbatively strong. The complex behaviour arising from this could,…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
In the study of non-adiabatic chemical processes such as photocatalysis and photosynthesis, non-adiabatic molecular dynamics (NAMD) is an indispensable theoretical tool, which requires precise potential energy surfaces (PESs) of ground and…
Semiconducting nanowires (NWs) are a versatile, highly tunable material platform at the heart of many new developments in nanoscale and quantum physics. Here, we demonstrate charge pumping, i.e., the controlled transport of individual…
The development of fast and strong microactuators that can be integrated in microdevices is an essential challenge due to a lack of appropriate driving principles. In this paper, a membrane actuator powered by internal combustion of…
Quantum computers have the potential to simulate chemical systems beyond the capability of classical computers. Recent developments in hybrid quantum-classical approaches enable the determinations of the ground or low energy states of…
Herein (the first part of my work), I debunk the long-standing hypotheses that explain mitochondrial oxidative phosphorylation. Simple calculations point out that mitochondria are highly proton-deficient microcosms and therefore, elaborate…
We have developed an excitation model for small molecules including radiative pumping by dust photons from near infrared to submillimeter wavelengths. This model applies to molecules within bright photodissociation regions in galactic…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…