Article
Multidisciplinary Sciences
Hongxia Hao, Itai Leven, Teresa Head-Gordon
Summary: Reaction rates of common organic reactions can significantly increase by several orders of magnitude in aqueous microdroplets compared to bulk solution. However, the reasons for this rate acceleration are still poorly understood. By studying the electric field distributions at the air-water interface, it has been found that the electric field alignments along free O-H bonds at the surface are on average around 16 MV/cm larger than those in the interior of the water droplet. This difference in electric field distribution may contribute to the enhanced surface reactivity observed in microdroplets.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Madhurima Chattopadhyay, Emilia Krok, Hanna Orlikowska, Petra Schwille, Henri G. Franquelim, Lukasz Piatkowski
Summary: The research introduces a new method to obtain dehydrated, phase-separated, supported lipid bilayers solely by controlling the decrease of relative humidity in the environment, facilitating the study of lipid bilayer structure and dynamics. The study shows that dehydration significantly affects lipid mobility, while the lipid domain structure of phase-separated SLBs remains largely unaffected by the presence of hydration layer.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Rahul Gera, Huib J. Bakker, Ricardo Franklin-Mergarejo, Uriel N. Morzan, Gabriele Falciani, Luca Bergamasco, Jan Versluis, Indraneel Sen, Silvia Dante, Eliodoro Chiavazzo, Ali A. Hassanali
Summary: This study investigates the properties of the water and surfactant C12E6 interface, finding that the addition of C12E6 near the critical micelle concentration enhances hydrogen bond strength and alters the orientation of water molecules. This leads to the formation of a broad interface with a large electric field, potentially opening up new possibilities for designing catalytic and light-harvesting systems at the water-surfactant-air interface.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Volker S. Urban, Raquel L. Lieberman, Wellington C. Leite, Yuqi Wu, Sai Venkatesh Pingali
Summary: This study investigates the impact of the single chain detergent DDM on the morphology of bicelles. DDM is able to reshape the bicelles at different temperatures, which is crucial for understanding lipid membrane self-organization and optimizing lipid mimics in membrane biology research.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Physics, Multidisciplinary
Marcio S. Gomes-Filho, Aline O. Pereira, Gustavo T. Feliciano, Luana S. Pedroza, Mauricio D. Coutinho-Neto
Summary: In this study, we propose a new method to construct a polarizable classical force field by using data from QM and QM/MM calculations to explain the charge redistribution at the water/metal interface. The method successfully reproduces the hexagonal ice layer structure in Pd(111)/water systems under low temperature conditions, as well as the metal-water interfacial tension at room temperature.
Article
Multidisciplinary Sciences
Yaolong Zhang, Bin Jiang
Summary: This study proposes a universal field-induced recursively embedded atom neural network (FIREANN) model that incorporates the effects of external fields on chemical structure and reactivity into machine learning models, demonstrating its potential for efficient first-principles modeling of complicated systems.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
Carlos Roberto de Souza Camilo, Jose Roberto Ruggiero, Alexandre Suman de Araujo
Summary: The cell membrane is crucial for understanding the efflux of substances between the cytoplasm and the environment. This study presents a method to detect water molecules permeation events through the lipid bilayer, providing valuable information about lipid interaction and permeability.
BRAZILIAN JOURNAL OF PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Amelie Bacle, Pavel Buslaev, Rebeca Garcia-Fandino, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. Fuchs, Ivan Gushchin, Matti Javanainen, Anne M. Kiirikki, Jesper J. Madsen, Josef Melcr, Paula Milan Rodriguez, Markus S. Miettinen, O. H. Samuli Ollila, Chris G. Papadopoulos, Antonio Peon, Thomas J. Piggot, Angel Pineiro, Salla Virtanen
Summary: Research shows that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, with differences in headgroup chemistry manifesting only in probability distributions of conformations. Furthermore, lipids can bind to proteins in a wide range of conformations, regardless of headgroup chemistry, suggesting that lipids can select a suitable headgroup conformation to fit the various binding sites in proteins. The proposed inverse conformational selection model is likely to extend to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Sheeba Malik, Ananya Debnath
Summary: Dehydration induces lipid bilayer ordering and slows down the dynamics of interface water molecules, displaying dynamical heterogeneity and glass-like dynamics. This study provides insights into the microscopic mechanism of lipid ordering under dehydration conditions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Hooman Hadidi, Reza Kamali
Summary: In this study, non-equilibrium molecular dynamics simulations were used to investigate the effects of external electric fields on the gating mechanism and water permeability of human aquaporin-2 (AQP2). The results showed that different directions of the electric field can lead to varied conformations of the selectivity filter region in AQP2, affecting water molecule translocation and permeability.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Haden L. Scott, Dima Bolmatov, Peter T. Podar, Zening Liu, Jacob J. Kinnun, Benjamin Doughty, Ralph Lydic, Robert L. Sacci, C. Patrick Collier, John Katsaras
Summary: This study demonstrates that droplet interface bilayers (DIBs) composed of lipids can exhibit persistent synaptic plasticity, characterized by long-term potentiation (LTP) and capacitive energy storage. The time scales for the physical changes associated with LTP are longer than previous short-term synaptic plasticity studies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Jie Wang, Xinxing Zhang
Summary: Research shows that at the air-water interface, the oxidation process of unsaturated and saturated fatty acid chains in phospholipids initiated by the photoinitiator 2,4,6-trimethylbenzoyl diphenylphosphine oxide (TMDPO) does not result in peroxidation products. A unique methodology called FIDI-MS is used to detect the products, revealing that double bonds on the oleyl chains are first oxidized into epoxides followed by oxidation of other saturated carbon atoms into carbonyl groups.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Materials Science, Multidisciplinary
A. T. N. Vo, M. A. Murphy, T. W. Stone, P. K. Phan, M. Baskes, R. K. Prabhu
Summary: Comparing MD simulations of biomolecules between GROMACS and LAMMPS revealed similar deformation behavior, but differences in pore nucleation, stress values, and damage values were observed. Various setting options and algorithm variations between the two software packages may explain these discrepancies.
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Le Luo, Swathi Manda, Yunjeong Park, Busra Demir, Jesse Sanchez, M. P. Anantram, Ersin Emre Oren, Ashwin Gopinath, Marco Rolandi
Summary: This study presents the integration of DNA nanopores with bioprotonic contacts to create programmable and efficient artificial ion-channel interfaces. This robust interface allows for electronic recognition and quantification of biomolecular signals.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Shinya Iwata, Hiroaki Uehara, Tatsuki Okamoto, Yasuo Sekii, Tatsuo Takada
Summary: This study investigated the diffusion properties of water and AP molecules in C120H242 chains through molecular dynamics simulations, and validated a proposed model for space charge formation and suppression mechanism for electrical degradation in polyethylene.
MATERIALS TODAY COMMUNICATIONS
(2021)
Meeting Abstract
Biophysics
Federica Castellani, Esin B. Sozer, P. Thomas Vernier
BIOPHYSICAL JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Esin B. Sozer, P. Thomas Vernier
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2019)
Review
Physics, Fluids & Plasmas
Martin Gundersen, P. Thomas Vernier, Stephen B. Cronin, Sanjana Kerketta
IEEE TRANSACTIONS ON PLASMA SCIENCE
(2020)
Article
Biochemistry & Molecular Biology
Nadica Ivosevic DeNardis, Galja Pletikapic, Ruza Frkanec, Lucija Horvat, P. Thomas Vernier
BIOELECTROCHEMISTRY
(2020)
Article
Biophysics
Esin B. Sozer, Sourav Haldar, Paul S. Blank, Federica Castellani, P. Thomas Vernier, Joshua Zimmerberg
BIOPHYSICAL JOURNAL
(2020)
Article
Biophysics
Josette Zaklit, Gale L. Craviso, Normand Leblanc, P. Thomas Vernier, Esin B. Sozer
Summary: The cellular effects of nanosecond-pulsed electric field exposures can be attenuated by bipolar pulse cancellation using equal duration and amplitude positive and negative phases, with response restoration achieved through appropriate interphase intervals. The modulation of Ca2+ responses in neural-type cells with ultrashort pulses demonstrates the potential for using nanosecond bipolar pulse technologies for neuromodulation applications.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Esin B. Sozer, Andrei G. Pakhomov, Iurii Semenov, Maura Casciola, Vitalii Kim, P. Thomas Vernier, Christian W. Zemlin
Summary: Short-duration, strong electric field pulses can be used for various applications, but nanosecond pulses require high field strengths. A theoretical model is presented to describe the effects of pulse trains on membranes, providing a method to calculate membrane charging time constant. Nanosecond pulses are found not more effective than longer pulses in charging nerve fibers, but considering multiple charging time constants improves the model's predictability for stimulating cardiomyocytes. The model also shows that pulse trains can cause significant oscillations of intracellular membrane potential.
BIOELECTROCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Josette Zaklit, Alex Cabrera, Aaron Shaw, Rita Aoun, P. Thomas Vernier, Normand Leblanc, Gale L. Craviso
Summary: The study found that under certain conditions, ultra-short electric pulses can stimulate the release of catecholamines through exocytosis, with real-time observations showing that the release is Ca2+-dependent and the release events are relatively prolonged. Furthermore, the effectiveness of this stimulation method was demonstrated, indicating its potential as a novel electrostimulation modality for neurosecretion.
BIOELECTROCHEMISTRY
(2021)
Meeting Abstract
Biophysics
Flavia Mazzarda, Esin B. Sozer, Claudia Muratori, P. Thomas Vernier
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Federica Castellani, Maria Laura Fernandez, Marcelo Risk, P. Thomas Vernier
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Flavia Mazzarda, Esin B. Sozer, Julia L. Pittaluga, Claudia Muratori, P. Thomas Vernier
BIOPHYSICAL JOURNAL
(2021)
Meeting Abstract
Biophysics
Federica Castellani, Tatiana Zvoraneva, Esin B. Sozer, P. Thomas Vernier
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Fluids & Plasmas
C. Jiang, E. B. Sozer, S. Song, N. Lai, P. T. Vernier, S. Guo
PHYSICS OF PLASMAS
(2020)
Meeting Abstract
Biophysics
Esin B. Sozer, Sourav Haldar, Federica Castellani, P. Thomas Vernier, Joshua Zimmerberg
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Federica Castellani, Esin B. Sozer, P. Thomas Vernier
BIOPHYSICAL JOURNAL
(2020)