6 papers
Exploring the use of quantum computing for facilitating spatially and temporally resolved models of a biological cell
Muralikrishnan Gopalakrishnan Meena, Dileep Kishore, Jerry M. Parks +5
Whole-cell simulation, modeling all of a cell's functional systems over its life cycle, is an outstanding challenge in computational biology. Even the simplest living cell contains…
Rotational Memory Function of SPC/E water
Dilipkumar N. Asthagiri, Dmitry V. Matyushov
Memory effects are essential for dynamics of condensed materials and are responsible for non-exponential relaxation of correlation functions of dynamic variables through the memory…
Equipartition and the temperature of maximum density of TIP4/2005 water
Dilipkumar N. Asthagiri, Thiago Pinheiro dos Santos, Thomas L. Beck
We simulate TIP4P/2005 water in the temperature range of 257 K to 318 K with time-steps 0.25, 0.50, 2.00, and 4.00 fs. The density-temperature behavior obtained using 0.25 or…
Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein
Dilipkumar N. Asthagiri, Arjun Valiya Parambathu, Thomas L. Beck
Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step fs to ensure equipartition betwe…
Quantifying the Errors Introduced by Continuum Scattering Models on the Inferred Structural Properties of Proteins
Rohan S. Adhikari, Dilipkumar N. Asthagiri, Walter G. Chapman
Atomistic force fields that are tuned to describe folded proteins predict overly compact structures for intrinsically disordered proteins (IDPs). To correct this, improvements in f…
System size dependence of hydration shell occupancy
D. Asthagiri, Dheeraj Singh Tomar
The free energies to evacuate the first hydration shell around a solute and a cavity defined by the first hydration shell depend on the system size. This observation interpreted wi…