| Integration of smFRET and molecular dynamics to characterize conformational dynamics of the spike protein of wild-type SARS-CoV-2 and its variants | Biophysical Journal | Abstract | 2023 |
| Atomic-level characterization of the human immunodeficiency virus type 1 envelope glycoproteins using molecular dynamic simulations | Biophysical Journal | Abstract | 2023 |
| Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel | Biophysical Journal | Abstract | 2023 |
| An integrative approach to molecular dynamics and single molecule FRET techniques | Biophysical Journal | Abstract | 2023 |
| Cholesterol concentration effect on bilayer membranes and its role in designing efficient liposomal drug delivery systems | Biophysical Journal | Abstract | 2023 |
| Cholesterol dependence on the conformational changes of metabotropic glutamate receptor 1 (mGLuR1) | Biophysical Journal | Abstract | 2023 |
| Structural effects of ALS-associated mutations on profiling | Biophysical Journal | Abstract | 2023 |
| Comparison of cyclic AMP binding activity within HCN channel subfamily using atomistic molecular dynamics simulations of isolated cyclic nucleotide binding domains | Biophysical Journal | Abstract | 2023 |
| A molecular dynamics study of the FGF1/FGF2 heterodimer in human fibroblasts | Biophysical Journal | Abstract | 2023 |
| cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach | Journal of Chemical Information and Modeling | Journal Article | 2023 |
| Addressing the Embeddability Problem in Transition Rate Estimation | Journal of Physical Chemistry A | Journal Article | 2023 |
| Cholesterol in Class C GPCRs: Role, Relevance, and Localization | Membranes | Journal Article | 2023 |
| The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs | Membranes | Journal Article | 2023 |
| Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters | Membranes | Journal Article | 2023 |
| Binding affinity estimation from restrained umbrella sampling simulations | Nature Computational Science | Journal Article | 2023 |
| Towards a purely physics-based computational binding affinity estimation | Nature Computational Science | Journal Article | 2023 |
| Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesis | Nanoscale Advances | Journal Article | 2022 |
| A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls | Journal of Chemical Theory and Computation | Journal Article | 2022 |
| An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations | Frontiers in Molecular Biosciences | Journal Article | 2022 |
| Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1 | Journal of Biological Chemistry | Journal Article | 2022 |
| Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins | bioRxiv | Journal Article | 2022 |
| Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel | Computational and Structural Biotechnology Journal | Journal Article | 2022 |
| Physics-based computational framework for absolute binding affinity estimation | Abstracts of Papers of the American Chemical Society | Abstract | 2022 |
| An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations | Biophysical Journal | Abstract | 2022 |
| Addressing the embeddability problem in transition rate estimation from Markov state models | Biophysical Journal | Abstract | 2022 |
| Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics | Biophysical Journal | Abstract | 2022 |
| Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoprotein | Biophysical Journal | Abstract | 2022 |
| Structural dynamics of prefusion spike protein of SARS-CoV-2 and its variants | Biophysical Journal | Abstract | 2022 |
| Using molecular dynamics simulations to characterize the structural/conformational effect of amino acid substitutions at the second position of the intrinsically disordered mitochondrial localization peptide (MLP) | Biophysical Journal | Abstract | 2022 |
| Molecular dynamics investigation of the ph-dependent influenza hemagglutinin conformational change | Biophysical Journal | Abstract | 2022 |
| Developing Efficient Transfer Free Energy Calculation Methods for Hydrophobicity Predictions | Biophysical Journal | Abstract | 2021 |
| Conformational Transition Pathway of GkPOT | Biophysical Journal | Abstract | 2021 |
| Differential Dynamic Behavior of Prefusion Spike Glycoproteins of Sars Coronaviruses 1 and 2 | Biophysical Journal | Abstract | 2021 |
| Integrating Molecular Dynamics and smFRET Data to Study the Conformational Ensemble of the C-Terminus of Albino3 Protein | Biophysical Journal | Abstract | 2021 |
| An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD Simulations | Biophysical Journal | Abstract | 2021 |
| Comparing the Dynamic Differences between X-ray and Cryo-EM Structures of Cannabinoid Receptor 1 using Molecular Dynamics Simulations | Biophysical Journal | Abstract | 2021 |
| Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes | Biophysical Journal | Abstract | 2021 |
| An Investigation of the Disulfide Bridge Formation of a Thylakoid Protease using Nanosecond-Level MD Simulations | Biophysical Journal | Abstract | 2021 |
| Investigation of Cyclic AMP Binding Interactions with Isolated Cyclic Nucleotide Binding Domain of HCN1 Channel using Atomistic Molecular Dynamics Simulations at Microsecond Timescale | Biophysical Journal | Abstract | 2021 |
| Differential thermodynamics and kinetics of prefusion spike proteins of SARS-CoV-1 and 2. | Abstracts of Papers of the American Chemical Society | Abstract | 2021 |
| Conformational free energy landscape of prefusion spike protein in SARS-CoV-1 and 2. | Abstracts of Papers of the American Chemical Society | Abstract | 2021 |
| Similarities and differences of conformational transition pathways in uniporters, symporters, and antiporters of the major facilitator superfamily of transporters. | Abstracts of Papers of the American Chemical Society | Abstract | 2021 |
| Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding | Journal of Physical Chemistry B | Journal Article | 2021 |
| Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus | Journal of Physical Chemistry B | Journal Article | 2021 |
| Structural Propensity in the C-terminal domain of the Albino3 translocase in thylakoids | Protein Science | Abstract | 2021 |
| Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor | Scientific Reports | Journal Article | 2021 |
| Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase | Biophysical Journal | Journal Article | 2021 |
| Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions. | Structure and Function of Membrane Proteins | Book Section | 2021 |
| Structural Propensity in the C-terminal Domain of the ALbino3 Translocase in Thylakoids | FASEB Journal | Abstract | 2020 |
| Differential dynamic behavior of prefusion spike proteins of SARS coronaviruses 1 and 2 | bioRxiv | Journal Article | 2020 |
| An Investigation of the YidC-Mediated Membrane Insertion of a Pf3 Coat Protein Using MD Simulations | Biophysical Journal | Abstract | 2020 |
| An Integrative Approach to Single-Molecule FRET Spectroscopy and Molecular Dynamics Simulations for the Study of Intrinsically Disordered Proteins | Biophysical Journal | Abstract | 2020 |
| An Investigation of the Influenza Hemagglutinin Membrane Fusion Process using Microsecond-Level MD Simulations | Biophysical Journal | Abstract | 2020 |
| Effect of Cholesterol on the Structural Dynamics of Metabotropic Glutamate Receptor (mGluR(1)): A Molecular Dynamics Study | Biophysical Journal | Abstract | 2020 |
| Binding Free Energy Calculations of NMDA Glutamate Receptors | Biophysical Journal | Abstract | 2019 |
| Mechanistic Study of a Peptidase Containing ABC-Transporter, Employing Microsecond Level Molecular Dynamics Simulations and Enhanced Sampling Techniques | Biophysical Journal | Abstract | 2019 |
| A Comprehensive Investigation of the Stabilization of Monomeric Hfgf1 by Heparin Hexasaccharide using Microsecond-Level MD Simulations and Enhanced Sampling Techniques | Biophysical Journal | Abstract | 2019 |
| Elucidating the Molecular Basis of pH-Triggered Activation of an Engineered Mechanosensitive Channel | Biophysical Journal | Abstract | 2019 |
| Overcoming the Embeddability Problem: A More Robust Calculation of Kinetic Information from Sparsely Sampled Molecular Dynamics Simulations | Biophysical Journal | Abstract | 2019 |
| Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter | ACS Central Science | Journal Article | 2019 |
| The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2 | Scientific Reports | Journal Article | 2019 |
| An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin | Scientific Reports | Journal Article | 2019 |
| ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation | Scientific Reports | Journal Article | 2018 |
| High school biology students use of visual molecular dynamics as an authentic tool for learning about modeling as a professional scientific practice | Biochemistry and Molecular Biology Education | Journal Article | 2018 |
| Lipid-Dependent Alternating Access Mechanism in ABC Exporters Revealed using Microsecond-Level Molecular Dynamics Simulations | Biophysical Journal | Abstract | 2018 |
| Microsecond-Level Simulations Reveal Membrane Protein Insertion Mechanism of Insertase YidC | Biophysical Journal | Abstract | 2018 |
| All-Atom Molecular Dynamics Simulation of Stealth Liposomes | Biophysical Journal | Abstract | 2017 |
| Couplings between Local and Global Conformational Changes in Proton-Coupled Oligopeptide Transporters | Biophysical Journal | Abstract | 2017 |
| Modeling the atomistic structure and dynamics of the chloroplast signal recognition particles | Abstracts of Papers of the American Chemical Society | Abstract | 2017 |
| Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases | Journal of the American Chemical Society | Journal Article | 2017 |
| What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT? | Journal of Physical Chemistry B | Journal Article | 2017 |
| Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems | Journal of Physical Chemistry Letters | Journal Article | 2016 |
| Conformational free energy landscape of inward- and outward-facing states of peptidase-containing ATP-binding cassette transporter PCAT1 | Abstracts of Papers of the American Chemical Society | Abstract | 2016 |
| A Riemannian Framework for Tackling Large-Scale Conformational Changes of Proteins using All-ATOM Molecular Dynamics Simulations | Biophysical Journal | Abstract | 2016 |
| Effective Riemannian diffusion model for conformational dynamics of membrane transporters | Abstracts of Papers of the American Chemical Society | Abstract | 2015 |
