Article
Chemistry, Physical
Max Lukas, Ralph Schwidetzky, Anna T. Kunert, Ellen H. G. Backus, Ulrich Poeschl, Janine Froehlich-Nowoisky, Mischa Bonn, Konrad Meister
Summary: Ice-nucleating proteins (INPs) from bacteria are highly effective at initiating ice formation near 0 degrees C. Research shows that INPs have a defined solution structure and do not undergo significant conformational changes upon cooling, but irreversible structural changes occur upon heating. Sum-frequency generation (SFG) spectroscopy reveals that active and heat-inactivated INPs have similar effects on ordering interfacial water molecules during cooling.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Liora E. Mael, Gordon Peiker, Heidi L. Busse, Vicki H. Grassian
Summary: By using micro-Raman spectroscopy, the study found that the equilibrium of partially and fully hydrogen-bonding water interactions changes as temperature decreases, leading to a phase transition to form ice. Furthermore, the thermodynamic parameters for the interchange between partially and fully hydrogen-bonded water for different types of supercooled droplets have been determined through temperature-dependent measurements.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Materials Science, Multidisciplinary
Elizabeth A. Delesky, Luis F. Garcia, Aparna J. Lobo, Rebecca A. Mikofsky, Nicolas D. Dowdy, Jaqueline D. Wallat, Garret M. Miyake, Wil V. Srubar
Summary: Ice growth mitigation is a challenge for multiple industries. Inspired by ice-binding proteins (IBPs), researchers have developed a bioinspired polymer, pHPMA, that shows strong ice recrystallization inhibition (IRI) activity at ultralow nanomolar concentrations. This study provides valuable insights into the synthesis and characterization of potent bioinspired materials that mimic the behavior of native IBPs.
ACS APPLIED POLYMER MATERIALS
(2022)
Article
Chemistry, Physical
Kartik Kamat, Pavithra M. Naullage, Valeria Molinero, Baron Peters
Summary: This paper presents a diffusion-controlled adsorption theory for long, helical antifreeze proteins (AFPs) binding at specific orientations to flat ice surfaces. The theory considers the complete geometry of the molecule and the orientational constraints for adsorption, and it is important for predicting the kinetics of crystal growth.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Akari Yamauchi, Ai Miura, Hidemasa Kondo, Tatsuya Arai, Yuji C. Sasaki, Sakae Tsuda
Summary: Research indicates that using a subzero supercooled solution containing insect AFP can significantly extend the preservation period of mammalian cells, with a higher survival rate, particularly the combination of -5 degrees C supercooling and insect AFP showing the best results.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Zulal Muganli, Shaghayegh Saeidiharzand, Regina Rekuviene, Vykintas Samaitis, Audrius Jankauskas, Ali Kosar, Ghazaleh Gharib, Abdolali Sadaghiani
Summary: Ice formation on solid surfaces poses challenges in industrial applications due to increased energy consumption and performance deterioration. Preparation of anti-icing surfaces using cryoprotectants is effective in reducing operational costs and extending surface lifespan. This study investigates the cloning, expression, and production of antifreeze proteins (AFPs) from E. Coli and their immobilization on aluminum surfaces. The coated AFP exhibits strong anti-icing ability on evaporator fins, highlighting the potential of AFPs for energy-saving and improved performance in various industrial applications.
ADVANCED MATERIALS INTERFACES
(2023)
Article
Chemistry, Physical
Aindrila Indra, Mangesh Bhendale, Jayant K. Singh
Summary: This study uses molecular dynamics to investigate the role of concentration, degree of supercooling, degree of polymerization, and amphiphilicity of PVA and PVA-like polymers on the homogeneous nucleation of water in dilute polymeric solutions. The results suggest that an increase in solute concentration decreases the nucleation rate of water, contradicting previous simulation studies.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Biochemistry & Molecular Biology
Abirami Baskaran, Manigundan Kaari, Gopikrishnan Venugopal, Radhakrishnan Manikkam, Jerrine Joseph, Parli Bhaskar
Summary: Antifreeze proteins are produced by organisms to adapt to extreme cold environments, protecting cells from ice crystal formation by lowering the freezing point of body fluids. These proteins, with diverse structures, modify ice crystal growth to thrive in cold conditions. Antifreeze proteins have a wide range of applications in industry, biomedicine, and food storage.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Prasun Pal, Sandipan Chakraborty, Biman Jana
Summary: This study investigates the specific binding of different types of antifreeze proteins to ice, along with the structure of their hydration layer and the properties of solvation water. It reveals that the hydration layer of globular AFP is semiclathrate-like, contrasting with the ice-like hydration layer of hyperactive AFP. These findings suggest a differential design in the ice-binding surface of antifreeze proteins that may contribute to their varying antifreeze activity.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Multidisciplinary Sciences
Steven J. Roeters, Thaddeus W. Golbek, Mikkel Bregnhoj, Taner Drace, Sarah Alamdari, Winfried Roseboom, Gertjan Kramer, Tina Santl-Temkiv, Kai Finster, Jim Pfaendtner, Sander Woutersen, Thomas Boesen, Tobias Weidner
Summary: The study reveals the structure of ice-active repeats of ice-nucleating proteins in solution and at water surfaces, as well as their reorientation at low temperatures, which enhances interactions with water molecules and promotes water ordering.
NATURE COMMUNICATIONS
(2021)
Review
Food Science & Technology
Xu Chen, Xiaodan Shi, Xixi Cai, Fujia Yang, Ling Li, Jinhong Wu, Shaoyun Wang
Summary: Ice-binding proteins (IBPs) show great potential as ice crystal growth inhibitors in frozen foods. This review focuses on the characteristics, structural diversity, and mechanisms of IBPs, as well as their application advances in the food industry.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2021)
Article
Multidisciplinary Sciences
Chanseok Lee, Yedam Lee, Woo Hyuk Jung, Tae-Yeon Kim, Taehwi Kim, Do-Nyun Kim, Dong June Ahn
Summary: Self-assembled DNA origami nanostructures can serve as cryoprotectant agents, protecting cells from damage during freeze-thaw cycles. Functionalized DNA nanopatches improve cell viability and exhibit minimal dependence on cryopreservation period and conditions.
Article
Chemistry, Multidisciplinary
Peng Zhang, Jingjing Li, Jing Sun, Yuanxin Li, Kai Liu, Fan Wang, Hongjie Zhang, Juanjuan Su
Summary: This study reports the creation of freezing tolerant protein fibers with favorable ice-phobic capacity and cryogenic mechanical performance through genetic engineering. These fibers, composed of chimeric recombinant proteins, exhibit excellent ice recrystallization inhibition activity and maintain remarkable mechanical properties and stability in subzero environments.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Marlene Davis Ekpo, Jingxian Xie, Yuying Hu, Xiangjian Liu, Fenglin Liu, Jia Xiang, Rui Zhao, Bo Wang, Songwen Tan
Summary: This review explores the potential clinical application of antifreeze proteins (AFPs) in the cryopreservation of different cells, tissues, and organs. It discusses novel approaches, identifies research gaps, and proposes future research directions for the successful clinical and commercial use of AFPs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Roderick P. Tas, Marco M. R. M. Hendrix, Ilja K. Voets
Summary: Antifreeze proteins (AFPs) have been found to bind ice and lower freezing temperatures, making them crucial for the survival of organisms in icy environments. However, there is still debate over the mechanisms through which they function. In this study, subzero nanoscopy was used to observe the dynamics of individual AFPs binding to ice crystals. The results provided experimental evidence for the adsorption-inhibition paradigm and highlighted the importance of reversible binding to ice in the overall model of AFP activity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Ethan F. Bull-Vulpe, Marc Riera, Sigbjorn L. Bore, Francesco Paesani
Summary: This study presents a generalization of the many-body energy framework, which can be used to develop data-driven potential energy functions for molecules with covalent bonds. By defining monomers as building blocks and using permutationally invariant polynomials to represent the energy, complex molecular systems can be simulated with arbitrary quantum mechanical accuracy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Yaoguang Zhai, Alessandro Caruso, Sigbjorn Loland Bore, Zhishang Luo, Francesco Paesani
Summary: Deep neural network (DNN) potentials have gained popularity in computer simulations of molecular systems. This study combines the computational efficiency of the DeePMD framework and the accuracy of the MB-pol potential to train a DNN potential for large-scale simulations of water. The DNN potential can reproduce MB-pol results for liquid water but lacks accuracy for vapor-liquid equilibrium properties. Attempts to include many-body effects result in a new DNN potential that accurately reproduces vapor-liquid equilibrium properties but loses accuracy in liquid properties.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Raja Ghosh, Francesco Paesani
Summary: Photoactive organic and hybrid organic-inorganic materials exhibit interesting photophysical properties upon interaction with light. A theoretical model that accurately describes the structure-photophysics-property relationships is crucial for understanding these materials. This perspective introduces a unified theoretical framework and discusses excitonic and polaronic photophysical signatures in different materials using the Multiparticle Holstein Formalism. The integration of advanced computational methods with the Multiparticle Holstein Formalism is expected to identify new design strategies for next-generation energy materials.
Article
Biophysics
Arpa Hudait, James H. Hurley, Gregory A. Voth
Summary: In the late stages of the HIV-1 life cycle, the membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. The release of the virion requires the interaction between Gag lattice and ESCRT machinery at the viral budding site, followed by the assembly of downstream ESCRT-III factors. However, the molecular details of upstream ESCRT assembly dynamics remain unclear. In this study, molecular simulations were used to investigate the interactions between Gag, ESCRT-I, ESCRT-II, and membrane, revealing the mechanisms by which upstream ESCRTs assemble at the viral budding site.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Brodie L. Ranzau, Kartik L. Rallapalli, Mallory Evanoff, Francesco Paesani, Alexis C. Komor
Summary: Base editors are genome editing tools that modify nucleobases in DNA to enable precise base conversions. Adenine base editors convert A.T base pairs to G.C base pairs by using an adenosine deaminase enzyme. Previous experiments showed that the wild-type TadA enzyme had no activity on DNA, but we demonstrated that it can perform base editing in both bacterial and mammalian cells.
Article
Chemistry, Physical
Xuanyu Zhu, Marc Riera, Ethan F. Bull-Vulpe, Francesco Paesani
Summary: Using the MB-pol theoretical/computational framework, we have introduced a new family of data-driven many-body potential energy functions (PEFs) for water, named MB-pol(2023). By employing larger training sets and adopting sophisticated machine-learned representations, the MB-pol(2023) PEFs achieve sub-chemical accuracy in modeling hexamer isomers and outperform existing PEFs in describing water clusters in the gas phase. Moreover, the MB-pol(2023) PEFs show remarkable agreement with experimental results for various properties of liquid water, improving upon the original MB-pol PEF and closing the gap with experimental measurements.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Baorui Cheng, Yu Zhong, Yuqing Qiu, Suriyanarayanan Vaikuntanathan, Jiwoong Park
Summary: Generating electricity from a salinity gradient, known as osmotic power, has been made possible with the development of ultrathin membranes that have molecule-specific short-range interactions. These membranes have demonstrated giant gateable osmotic power with a record high power density. Molecular dynamics simulations have confirmed that the functionalized nanopores in these membranes are small enough for high selectivity and large enough for fast cross-membrane transport, enabling reversible gateable operation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Thomas M. Rayder, Filip Formalik, Simon M. Vornholt, Hilliary Frank, Seryeong Lee, Maytham Alzayer, Zhihengyu Chen, Debabrata Sengupta, Timur Islamoglu, Francesco Paesani, Karena W. Chapman, Randall Q. Snurr, Omar K. Farha
Summary: Carbon capture, storage, and utilization (CCSU) is an opportunity to reduce carbon emissions and combat global climate change. Metal-organic frameworks (MOFs) have shown great potential as effective CO2 sorbents in CCSU through gas adsorption. Understanding the properties of MOF pores and their dynamic behavior during sorption can lead to the development of more efficient CCSU materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Sigbjrn Lland Bore, Francesco Paesani
Summary: Since the early 1900s, scientists have been trying to understand the stability of ice polymorphs in water's phase diagram. This study combines the MB-pol data-driven many-body potential for water with advanced enhanced-sampling algorithms to simulate water's phase diagram with a high level of realism. The study provides insights into the role of enthalpic, entropic, and nuclear quantum effects in shaping the free-energy landscape of water and bridges the gap between experiments and simulations.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Ching-Hwa Ho, Mason L. L. Valentine, Zhijie Chen, Haomiao Xie, Omar Farha, Wei Xiong, Francesco Paesani
Summary: This study investigates the water adsorption mechanism in the hydrophilic metal-organic framework NU-1500-Cr using molecular dynamics simulations and infrared spectroscopy. It is found that water initially adsorbs at the open Cr3+ sites and then forms water chains that gradually fill the framework. The insights gained from this study can contribute to the design of efficient water harvesting materials.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Physical
Yuanhui Pan, Ching-Hwa Ho, Francesco Paesani, Raja Ghosh
Summary: Covalent organic frameworks (COFs) are 2D organic materials with unique electronic and transport properties. In this study, the impact of interlayer stacking arrangements on the electronic structure and coherence of polarons in donor-acceptor COFs was investigated through density functional theory and multiparticle Holstein formalism simulations. It was found that the stacking arrangement significantly influences the transport properties, with varying behavior from metallic to highly localized states. The extent of charge delocalization is sensitive to the type and precise arrangement of interlayer stacking and donor-acceptor fragments in the COF structure. The results suggest that interlayer interactions can aid in enhancing charge delocalization and guide the design of new COF structures for potential applications in organic electronics.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Physical
Marc Riera, Christopher Knight, Ethan F. Bull-Vulpe, Xuanyu Zhu, Henry Agnew, Daniel G. A. C. Smith, Andrew Simmonett, Francesco Paesani
Summary: MBX is a C++ library that implements many-body potential energy functions (PEFs) within the many-body energy (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be used as a standalone package or integrated with other molecular simulation software as an energy/force engine. It allows for classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations combining conventional force fields and MB-nrg PEFs for diverse systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Ruihan Zhou, Marc Riera, Francesco Paesani
Summary: We introduce a data-driven many-body energy potential energy function (MB-nrg PEF) to accurately describe the energetics and structural properties of N-methylacetamide (NMA), as well as the NMA-water interactions. The results show that the MB-nrg PEF is able to accurately represent many-body effects in both gas and liquid phases, making it a promising molecular model for predictive simulations of biomolecular systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Materials Science, Multidisciplinary
Zhihengyu Chen, Ching-Hwa Ho, Xiaoliang Wang, Simon M. Vornholt, Thomas M. Rayder, Timur Islamoglu, Omar K. Farha, Francesco Paesani, Karena W. Chapman
Summary: CALF-20, a metal-organic framework, shows selective CO2 physisorption. This study reveals that CALF-20 undergoes a structure transformation when exposed to humid environments, resulting in a new polymorph. The transformation is reversible, and the original structure can be regenerated. Computational evaluation indicates that the new polymorph has a higher CO2 heat of adsorption, potentially leading to improved CO2 sorption selectivity at low partial pressures.
ACS MATERIALS LETTERS
(2023)
Article
Materials Science, Multidisciplinary
Jierui Zhang, Francesco Paesani, Martina Lessio
Summary: Studies have shown that incorporating hydrophilic functional groups into the UiO-66 metal-organic framework (MOF) can improve its water uptake ability at low relative humidity (RH). This computational study provides insights into the adsorption mechanism of water in UiO-66 and its functionalized derivatives, revealing the preferential interaction sites and the formation of localized water clusters inside the octahedral pores. The presence of functional groups allows water to cluster in the pores at lower RH, making the MOF a more efficient water harvester.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)