Article
Chemistry, Medicinal
Christophe Chipot
Summary: Predicting the rate of passive permeation of small molecules across the biological membrane is a promising strategy for drug discovery. The estimation of permeation rates through computer simulations and the solubility-diffusion model requires determining the free-energy change and diffusivity of the substrate along the translocation pathway. This Perspective clarifies the physical meaning of membrane permeability from computer simulations and discusses the challenges and potential research directions to improve the predictive power and practical usefulness of physics-based rates of passive permeation.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Materials Science, Multidisciplinary
Haechan Park, Shuanglong Liu, James N. Fry, Hai-Ping Cheng
Summary: In this study, the magnetic interactions between Mn atoms in bilayer manganese phthalocyanine (MnPc) molecules and MnPc polymeric sheets were investigated using first-principles simulations. The Neel antiferromagnetic (AFM) configuration within a layer and ferromagnetic (FM) configuration between Mn atoms in adjacent layers was found to be the magnetic ground state. The strongest interaction was identified as the interlayer coupling between the closest Mn atoms.
Article
Engineering, Chemical
Keita Yano, Masayuki Iwamoto, Takaaki Koshiji, Shigetoshi Oiki
Summary: This study establishes an accurate method for evaluating the osmotic permeability of lipid bilayers under constant tension, and known unstirred layers. This method helps to better understand the water flux process across cell membranes by quantifying membrane tension and unstirred layers.
JOURNAL OF MEMBRANE SCIENCE
(2021)
Article
Chemistry, Physical
Qiang Fan, Weibin Zhang, Haiyin Qing, Jianhui Yang
Summary: The geometry, vibrational, electronic, and thermoelectric properties of bilayer GeSe, bilayer SnSe, and vdW heterostructure GeSe/SnSe are investigated using first-principles calculations and semiclassical Boltzmann transport theory. The results show that bilayer GeSe and GeSe/SnSe structure are stable with indirect band gaps. Furthermore, n-type bilayer GeSe exhibits promising thermoelectric performance.
Article
Materials Science, Multidisciplinary
Zhe Wang, Zhigang Gui, Li Huang
Summary: The sliding ferroelectricity in artificially stacked nonpolar two-dimensional (2D) materials greatly expands the range of 2D ferroelectrics. However, the electric polarizations are generally small due to weak van der Waals interlayer interaction. Discovering 2D sliding ferroelectrics with large polarization remains a challenge.
Article
Chemistry, Physical
Liucheng Liu, Shengfeng Zhou, Haoran Gong
Summary: This study comparatively examines the hydrogen behavior at PdCu(110)-Mo2C(001) interfaces using first principles calculations. It is found that adding Mo2C as a coating and support can increase the hydrogen solubility of a BCC PdCu membrane. However, the formation of PdCu(110)-Mo2C(001) interfaces hinders hydrogen diffusion. The results provide insights into the effects of interface formation on hydrogen behaviors and suggest Mo2C/PdCu composite membranes as promising candidates for hydrogen permeation.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Chemistry, Physical
Hongyue Song, Xuehua Zhang, Peiling Yuan, Wencheng Hu, Zhibin Gao
Summary: By using first-principles calculations and theoretical analysis, we found that the bilayer SnP3 has high carrier mobility and Seebeck coefficient, as well as extremely low phonon thermal conductivity. This makes the bilayer SnP3 a promising thermoelectric material with better performance than its monolayer phase and SnSe.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Derek S. Wang, Susanne F. Yelin, Johannes Flick
Summary: This study demonstrates how to tune the optical properties of defects in solid-state materials via the formation of defect polaritons in an optical cavity from first principles. It shows significant polaritonic splitting and absorption intensity enhancement, potentially overcoming phonon-limited single-photon emission from defect centers. These findings are expected to inspire experimental investigations of strong light-matter coupling between defect centers and cavity photons for applications in quantum technologies.
Article
Multidisciplinary Sciences
Jussi Lehtonen
Summary: This article reviews the experiments and concepts presented by Angus Bateman in 1948 regarding sexual selection and the Bateman gradient. The study develops mathematical models showing that asymmetry in gamete numbers alone can generate steeper Bateman gradients in males. The research provides evidence for Bateman's claim about the role of gamete numbers in sexual selection.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Dibya Prakash Rai, Bhanu Chettri, Prasanta Kumar Patra, Shahid Sattar
Summary: Using first-principles calculations, the study investigates the structural and electronic properties of bilayer hexagonal boron nitride (h-BN) with hydrogen (H-2) molecules for potential H-2-storage applications. The decrease in binding energies and desorption temperatures, along with the role of different density functionals in understanding energy gaps and molecular adsorption, are highlighted in the research findings, providing insights into the potential of bilayer h-BN in hydrogen-based energy-storage applications.
Article
Chemistry, Multidisciplinary
Arash Manafirad, Cintia A. Menendez, Gustavo R. Perez-Lemus, S. Thayumanavan, Juan J. de Pablo, Anthony D. Dinsmore
Summary: This study investigates the effects of optical control of phospholipids on membrane structure and dynamics. Experimental results and simulations show that isomerization can change the molecular area, stretching modulus, and water permeability of the membrane, which is significant for photopharmacology and material development.
Article
Materials Science, Multidisciplinary
Cong Wang, Guoying Gao, Hezhu Shao, Ke Xu
Summary: Recently, the WSe2/SnS2 van der Waals bilayer heterostructure has been found to have excellent electronic and optoelectronic applications. However, its thermoelectric properties have not been studied. In this study, we used first-principles calculations and Boltzmann transport theory to investigate the thermoelectric transport properties of the WSe2/SnS2 bilayer heterostructure. The results show that the n-type power factor of the WSe2/SnS2 bilayer heterostructure is greatly improved compared to that of the WSe2 monolayer. The optimized n-type thermoelectric ZT value at 800 K for WSe2/SnS2 can reach 1.16, indicating its promise for thermoelectric applications.
RESULTS IN PHYSICS
(2023)
Article
Electrochemistry
Muhammad Isa Khan, Sheeza Aslam, Abdul Majid, Syed Sajid Ali Gillani
Summary: By intercalating lithium into bilayer buckled borophene, the anode material showed improved adsorption energy, theoretical capacity, and diffusion barrier, while maintaining the metallic nature of borophene. The absence of volume expansion in fully lithiated structure, along with theoretical capacity of 1859 mAh/g, diffusion barrier of 80 eV, and OCV of 0.08 V, indicates the potential of bilayer b-borophene as a candidate for anode material in Li-ion batteries.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2021)
Article
Biochemical Research Methods
Nandan Kumar, G. Narahari Sastry
Summary: This study investigates the composition and structure-function relationships of lipids in human cell membranes. It was found that membranes enriched with cholesterol exhibit increased compactness and thickness.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Engineering, Chemical
Li-Jen Lin, Mukesh Saini, Chung-Jen Chiang, Yun-Peng Chao
Summary: In this study, a whole cell biocatalysis system was used to produce short-chain alcohols from fatty acids. Escherichia coli strain was reprogrammed to improve biocatalytic activity, resulting in successful production of 1-propanol and n-pentanol.
Article
Food Science & Technology
Lina Maria Preciado, Jaime Andres Pereanez, Jeffrey Comer
Article
Chemistry, Medicinal
Genoveva Rojas, Ivana Orellana, Roberto Rosales-Rojas, Jennie Garcia-Olivares, Jeffrey Comer, Ariela Vergara-Jaque
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Biochemistry & Molecular Biology
Jeffrey Comer, Molly Bassette, Riley Burghart, Mayme Loyd, Susumu Ishiguro, Ettayapuram Ramaprasad Azhagiya Singam, Ariela Vergara-Jaque, Ayaka Nakashima, Kengo Suzuki, Brian V. Geisbrecht, Masaaki Tamura
Summary: This study suggests that beta-1,3 glucans may stimulate T cell activation collaboratively with T cell receptor activation, thereby enhancing immune function. The research found that beta-1,3 oligoglucans bind to CD28 near the region identified as the binding site for its natural ligands CD80 and CD86, with a specific dissociation constant calculated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Nutrition & Dietetics
Deepa Upreti, Susumu Ishiguro, Nicole Robben, Ayaka Nakashima, Kengo Suzuki, Jeffrey Comer, Masaaki Tamura
Summary: This study evaluated the antitumor effects of partially purified water extracts from Euglena gracilis and found that it attenuated lung carcinoma growth by altering the intestinal microbiota.
Article
Engineering, Chemical
Yuntao Zhang, Ran Chen, Jim E. Riviere, Jeffrey Comer
Summary: Metal oxide nanoparticles show potential for selective adsorption and catalytic degradation of contaminants. Both experiments and simulations in this study reveal that chlorobenzenes and PCBs exhibit different adsorption behaviors towards zinc oxide nanoparticles, with the number of chlorine atoms playing a key role. The simulations predict that dioxin-like PCBs have the highest adsorption affinities for ZnO NPs.
Article
Chemistry, Medicinal
Justin Legleiter, Ravindra Thakkar, Astrid Velasquez-Silva, Ingrid Miranda-Carvajal, Susan Whitaker, John Tomich, Jeffre y Comer
Summary: The graphite-water interface provides a unique environment for the formation of ordered structures in polypeptides. This study computationally designed cyclic peptides that spontaneously fold into a beta-sheet-like conformation at the graphite-water interface and self-assemble. Experimental validation using atomic force microscopy confirmed the formation of linear patterns consistent with the simulations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Hao Deng, Jeffrey Comer, Bin Liu
Summary: A high-dimensional neural network interatomic potential was developed for molecular dynamics simulations of condensed phase Ni and Ni systems with liquid-solid phase coexistence. Accurate descriptions of the liquid-solid phase coexistence and phase transition behavior were achieved.
MOLECULAR SIMULATION
(2023)
Article
Biochemistry & Molecular Biology
Ravindra Thakkar, Dilip K. Agarwal, Chathuranga B. Ranaweera, Susumu Ishiguro, Martin Conda-Sheridan, Natasha N. Gaudreault, Juergen A. Richt, Masaaki Tamura, Jeffrey Comer
Summary: Despite the development of effective vaccines, low vaccination rates and new variants with spike protein mutations have reduced the effectiveness of current treatments against SARS-CoV-2. A 17-residue peptide called pep39 has been designed to block the interaction between the spike protein and the host's ACE2 receptor, using protein design software and molecular dynamics simulations. Experimental methods have confirmed the binding activity of pep39 to both the original spike protein and the delta variant, and it has shown strong inhibition of SARS-CoV-2 replication in cells. These findings suggest that pep39 has potential as a SARS-CoV-2 inhibitor.
RSC MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Matias Zuniga-Bustos, Jeffrey Comer, Horacio Poblete
Summary: Nanoscale silver particles are widely used in biomedical and other technologies due to their unique antibacterial, optical, and electrical properties. Understanding the structure and thermodynamics of capping agent layers on the metal surface is crucial for the preparation and protection of these nanoparticles.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Ravindra Thakkar, Deepa Upreti, Susumu Ishiguro, Masaaki Tamura, Jeffrey Comer
Summary: Proteins involved in immune checkpoint pathways, such as CTLA4, PD1, and PD-L1, have become important targets for cancer immunotherapy. The development of small molecule drugs targeting these pathways has proven difficult. In this study, a cyclic peptide (cyc(EIDTVLTPTGWVAKRYS)) is designed using computational techniques and verified experimentally for its binding and biological activity against CTLA4. The peptide inhibits tumor growth in co-culture of Lewis lung carcinoma (LLC) cells and antigen primed T cells, as well as in mice with an orthotropic LLC allograft model.
RSC MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Justin Legleiter, Ravindra Thakkar, Astrid Velasquez-Silva, Ingrid Miranda-Carvajal, Susan Whitaker, John Tomich, Jeffrey Comer
Summary: The graphite-water interface provides a unique environment for the folding and self-assembly of polypeptides, making it a convenient medium for controlled self-assembly of functional materials. In this study, cyclic peptides that fold and self-assemble at the graphite-water interface were computationally designed and their assembly was observed by atomic force microscopy. The optimized peptide showed spontaneous folding and self-assembly at the graphite-water interface under various conditions, and the stability of the folded conformation was verified by simulations and calculations. The self-assembly of folded peptides was promoted by intermolecular hydrogen bonds, resulting in linear arrangements along the zigzag directions of the graphite basal plane.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Diana M. Arvelo, Manuel R. Uhlig, Jeffrey Comer, Ricardo Garcia
Summary: This study investigated the evolution of the graphite-water interface using 3D AFM and found the presence of short-lived hydration layers followed by stable molecular layers. Molecular dynamics calculations supported the experimental observations.
Article
Nanoscience & Nanotechnology
Huihua Xing, Alison Rodger, Jeffrey Comer, Agustin S. Picco, Cristian Huck-Iriart, Edward L. Ezell, Martin Conda-Sheridan
Summary: This study investigates the effect of replacing the amide linkage between the peptide and lipid portions of peptide amphiphiles (PAs) with a urea group. The inclusion of the urea group is found to influence the morphology and internal arrangement of the self-assembled structures formed by the PAs. Additionally, the hydrogel made of the urea-modified PAs exhibits increased stability, self-healing ability, and supports cell adhesion and growth.
ACS APPLIED BIO MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Ravindra Thakkar, Sandun Gajaweera, Jeffrey Comer
Summary: Ordered nanoscale patterns observed on graphene, graphite, and other hydrophobic materials in water are likely due to the presence of alkane-like molecules at the interface.
NANOSCALE ADVANCES
(2022)
Article
Chemistry, Multidisciplinary
Manuel R. Uhlig, Simone Benaglia, Ravindra Thakkar, Jeffrey Comer, Ricardo Garcia
Summary: Hydration layers form on hydrophilic and hydrophobic crystalline surfaces, but on hydrophobic surfaces, water molecules are expelled and replaced by hydrocarbon molecules near the surface, creating a new interfacial layer.