Siva Dasetty- PhD
- PostDoc Position at University of Chicago
Siva Dasetty
- PhD
- PostDoc Position at University of Chicago
About
22
Publications
2,154
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203
Citations
Introduction
Graduated in 2019 with PhD from Sarupria group, Department of Chemical Engineering at Clemson University, where I contributed to the advancement of computer aided protein engineering.
Currently a postdoc in Ferguson lab, PME, University of Chicago where I am contributing to exploration of assembly of like charged dielectric nanoparticles, a novel ML based solution to tackle one of the grand challenges in water.
Current institution
Education
August 2013 - August 2015
August 2013 - August 2019
Publications
Publications (22)
Understanding peptide-surface interactions is crucial for programming self-assembly of peptides at surfaces and in realizing their applications, such as biosensors and biomimetic materials. In this study, we developed insights into the dependence of a residue's interaction with a surface on its neighboring residue in a tripeptide using molecular dy...
Polarizable nanoparticles are of interest in materials science because of their rich and complex phase behavior that can be used to engineer nanostructured materials with long-range crystalline order. To understand...
The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques...
Differences in the structural and thermodynamic properties of enzymes adapted to different temperatures indicate that broad range temperature active enzymes can be designed by incorporating cold activity in thermophilic enzymes....
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in...
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited i...
Widespread, persistent, and toxic per- and polyfluoroalkyl substances (PFAS) pose a major threat to both water systems and human health. Current PFAS detection methods are relatively expensive, slow, and complex. To combat PFAS contamination and meet increasingly stringent regulations of PFAS in drinking water, the development of highly sensitive a...
Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5’-triphosphate)...
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a br...
Molecular dynamics simulations are a core element of research in physics, chemistry and biology. A key aspect for extending the capability of simulation tools is providing access to advanced sampling methods and techniques that permit calculation of the relevant, underlying free energy landscapes. In this sense, software tools that can be seamlessl...
While thermophilic enzymes have thermostability desired for broad industrial applications, they can lose activity at ambient temperatures far from their optimal temperature. Engineering cold activity into thermophilic enzymes has the potential to broaden the range of temperatures resulting in significant activity (i.e., decreasing the temperature d...
While thermophilic enzymes have thermostability desired for broad industrial applications, they can lose activity at ambient temperatures far from their optimal. Engineering cold activity into thermophilic enzymes has the potential to broaden the range of temperatures resulting in significant activity (i.e., decreasing the temperature dependence of...
Interfacial systems are ubiquitous and important to myriad processes of interest such as protein-protein interactions and catalysis of reactions. Investigating interfacial systems at the molecular level presents unique challenges to both experiments and molecular simulations. The challenges in molecular simulations of interfacial systems range from...
We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnit...
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We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ...
Lipases are enzymes that hydrolyze lipids and have several industrial applications. There is a tremendous effort in engineering the activity, specificity and stability of lipases to render them functional in a variety of environmental conditions. In this review, we discuss the recent experimental and simulation studies focused on engineering lipase...
In any physiological media, carbon nanomaterials (CNM) strongly interact with biomolecules leading to the formation of biocorona, which subsequently dictate the physiological response and the fate of CNMs. Defects in CNMs play an important role not only in material properties but also in the determination of how materials interact at the nano-bio i...
A transient 2D axi-symmetric and lumped parameter (LP) model with constant outflow conditions have been developed to study the discharge capacity of an activated carbon bed. The predicted discharge times and variations in bed pressure and temperature are in good agreement with experimental results obtained from a 1.82 l adsorbed natural gas (ANG) s...
