• Understanding the translocation of fluoroquinolones through OmpC using the metadynamics 

  Prajapati, Jigneshkumar D. (Cell Press, 2015-01)

  The outer membrane of Gram-negative bacteria such as Escherichia coli acts as a selective permeable barrier between cell and external environment. Water filled outer membrane proteins called as porins were identified for ...
• Atomistic modeling of two-dimensional electronic spectra and excited-state dynamics for a light harvesting 2 complex 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2015-01)

  The Light Harvesting 2 (LH2) complex is a vital part of the photosystem of purple bacteria. It is responsible for the absorption of light and transport of the resulting excitations to the reaction center in a highly efficient ...
• Outer-membrane translocation of bulky small molecules by passive diffusion 

  Prajapati, Jigneshkumar Dahyabhai (Proceedings of the National Academy of Sciences, 2015-04)

  The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM ...
• Role of electroosmosis in the permeation of neutral molecules: CymA and cyclodextrin as an example 

  Prajapati, Jigneshkumar Dahyabhai (Cell Press, 2016-02)

  To quantify the flow of small uncharged molecules into and across nanopores, one often uses ion currents. The respective ion-current fluctuations caused by the presence of the analyte make it possible to draw some conclusions ...
• Electro-osmotic driven kinetics of cyclodextrin through the cyma channel 

  Prajapati, Jigneshkumar Dahyabhai (Cell Press, 2016-02)

  Trans membrane voltage is applied to understand the permeation of uncharged molecules into and across nano pores in Electrophysiology. The permeating molecule blocks the ion flow causing ion current fluctuations. However ...
• Biophysical insight into the substrate permeation through the major outer membrane channels of acinetobacter baumannii 

  Prajapati, Jigneshkumar Dahyabhai (Cell Press, 2017-02)

  Among other mechanisms the cause for Multidrug Resistant (MDR) bacteria is their reduced permeability for antibiotics in particular in Gram-negative bacteria such as Acinetobacter baumanii. Owing to the low permeability ...
• Effect of electroosmotic flow on the transport of α-cyclodextrin through the channel CymA 

  Prajapati, Jigneshkumar Dahyabhai (Elsevier, 2017-02)

  CymA, an outer membrane channel of Klebsiella oxytoca, allows the passive diffusion of the bulky molecule α-cyclodextrin (α-CD, M.W. 972.8 Da) to the periplasm of the bacterium [1]. In single channel electrophysiology ...
• Characterization of ciprofloxacin permeation pathways across the Porin OmpC using metadynamics and a string method 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2017-08)

  The rapid spreading of antimicrobial resistance in Gram-negative bacteria has become a major threat for humans as well as animals. As one of the main factors involved, the permeability of the outer membrane has attracted ...
• Enrofloxacin permeation pathways across the porin OmpC 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2018-01)

  In Gram-negative bacteria, the lack or quenching of antibiotic translocation across the outer membrane is one of the main factors for acquiring antibiotic resistance. An atomic-level comprehension of the key features ...
• Understanding the structure and function of the Dcap channel from acinetobacter baumannii using MD simulations 

  Prajapati, Jigneshkumar D. (Elsevier, 2018-02)

  DcaP is putative dicarboxylate specific channel, located in the outer membrane of the pathogen Acinetobacter baumannii. The X-ray crystal structure reveals that DcaP is the first trimeric channel identified in Acinetobacter ...
• Brownian dynamics approach including explicit atoms for studying ion permeation and substrate translocation across nanopores 

  Prajapati, Jigneshkumar D. (ACS, 2018-11)

  A Brownian dynamics (BD) approach including explicit atoms called BRODEA is presented to model ion permeation and molecule translocation across a nanopore confinement. This approach generalizes our previous hybrid molecular ...
• Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations 

  Prajapati, Jigneshkumar Dahyabhai (Elsevier, 2018-11)

  Although a multitude of theoretical studies exist on light-harvesting complex 2 (LH2), less is known about the light-harvesting complex 3 (LH3) of similar ring-like structure. In a comparative study of three system, i.e., ...
• A multidisciplinary approach toward identification of antibiotic scaffolds for acinetobacter baumannii 

  Prajapati, Jigneshkumar Dahyabhai (Elsevier, 2019-02)

  Research efforts to discover potential new antibiotics for Gram-negative bacteria suffer from high attrition rates due to the synergistic action of efflux systems and the limited permeability of the outer membrane (OM). ...
• Molecular interactions of cephalosporins with the deep binding pocket of the RND transporter AcrB 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2019-05)

  The drug/proton antiporter AcrB, part of the major efflux pump AcrABZ-TolC in Escherichia coli, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multidrug resistance ...
• Dynamic interaction of fluoroquinolones with magnesium ions monitored using bacterial outer membrane nanopores 

  Prajapati, Jigneshkumar Dahyabhai (RSC, 2020-08)

  Divalent ions are known to have a severe effect on the translocation of several antibiotic molecules into (pathogenic) bacteria. In the present study we have investigated the effect of divalent ions on the permeability of ...
• Exploration of free energy surfaces across a membrane channel using metadynamics and umbrella sampling 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2020-03)

  To reach their site of action, it is essential for antibiotic molecules to cross the bacterial outer membrane. The progress of enhanced sampling techniques in molecular dynamics simulations enables us to understand these ...
• Dynamic interaction of norfloxacin to magnesium monitored by bacterial outer membrane nanopores 

  Prajapati, Jigneshkumar Dahyabhai (2020-05)

  The effect of divalent ions on the permeability of norfloxacin across the major outer membrane channels from E. coli (OmpF, OmpC) and E. aerogenes (Omp35, Omp36) has been investigated at the single channel level. To ...
• Computational modeling of ion transport in bulk and through a nanopore using the drude polarizable force field 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2020-06)

  In the past two decades, molecular dynamics simulations have become the method of choice for elucidating the transport mechanisms of ions through various membrane channels. Often, these simulations heavily rely on classical ...
• DFTB/MM molecular dynamics simulations of the FMO light-harvesting complex 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2020-09)

  Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum–classical description. To this end, ...
• Voltage-dependent transport of neutral solutes through nanopores: a molecular view 

  Prajapati, Jigneshkumar Dahyabhai (ACS, 2020-11)

  The permeation of (neutral) molecules through nanopores in the presence of external voltages depends on several factors including pore electrostatics, electrophoretic force, and electro-osmotic drag. In earlier single-channel ...

View more