Article
Biochemistry & Molecular Biology
Manish Bajaj, Mohd Muddassir, Bumjoon Choi, Priyanka Singh, Jong Bum Park, Surjeet Singh, Manisha Yadav, Rajesh Kumar, Kilho Eom, Deepak Sharma
Summary: This study investigates the effect of osmolytes on the mechanical unfolding properties of protein domain using atomic force microscopy. The results show that amines and methylamines enhance the mechanical stability of the protein, while polyols have no effect. Glycine betaine and trimethylamine-N-oxide increase the average unfolding force of the protein domain. These findings have potential applications in modulating the mechanical stability of proteins for nano-biotechnological purposes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biology
Nicola Galvanetto, Zhongjie Ye, Arin Marchesi, Simone Mortal, Sourav Maity, Alessandro Laio, Vincent Torre
Summary: Single-molecule force spectroscopy (SMFS) is used to study protein unfolding, and we propose a pipeline for analyzing membrane proteins using SMFS. The pipeline involves isolating the plasma membrane of single cells and directly testing force-distance curves, combining information from mass spectrometry and proteomic databases to identify and characterize membrane proteins and classify their unfolding.
Article
Biochemical Research Methods
Yiming Bu, Long Yu, Pengchen Su, Lingxiao Wang, Zhenli Sun, Mingtai Sun, Xiangke Wang, Dejian Huang, Suhua Wang
Summary: Green-emitting carbon quantum dots were prepared successfully with a simple method, showing good fluorescence stability in aqueous solution. These carbon quantum dots exhibited high sensitivity and selectivity for detecting hypochlorite, and were successfully applied in determining hypochlorite in actual water samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Varsha Raveendran, Renuka Neeroli Kizhakayil
Summary: This study focuses on the versatile applications of carbon dots derived from Mint leaf extract, including biosensing, reduction, and biomarker functions. The carbon dots show high selectivity for detecting folic acid through fluorescent sensing, and are effective in reducing Fe(III) and synthesizing noble metal nanoparticles.
Article
Engineering, Civil
Cao Yingri, Wang Haishen, Sun Jiangbo, Pan Peng
Summary: This paper presents a novel two-direction shear-force sensor (2D-SFS) for measuring boundary friction force in structural compression-shear tests. The sensor is capable of measuring both friction force and shear force, and enhances test accuracy through horizontal force correction.
ENGINEERING STRUCTURES
(2022)
Article
Biotechnology & Applied Microbiology
Guo-Teng Liang, Cuixin Lai, Zejun Yue, Hanbin Zhang, Danyang Li, Zhong Chen, Xingyu Lu, Liang Tao, Fedor V. Subach, Kiryl D. Piatkevich
Summary: In this study, a pair of engineered flavin-binding fluorescent proteins, miniGFP1 and miniGFP2, were developed. These miniGFPs showed improved photochemical properties and high sensitivity to transition metal ions, making them potential fluorescent biosensors for live cell imaging and metal ion detection.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Narayan Dahal, Sabita Sharma, Binh Phan, Annie Eis, Ionel Popa
Summary: The study found that the R8 domain of talin displays memory-dependent behavior under force, indicating the evolution of a unique force-induced native state. It was also discovered that talin R8 domain binds its ligand DLC1 with much higher affinity than previously reported. This interaction may explain the anti-tumor response of DLC1 by regulating the inside-out activation of integrins.
Article
Chemistry, Multidisciplinary
Ziqing Tang, Huacheng He, Lin Zhu, Zhuangzhuang Liu, Jia Yang, Gang Qin, Jiang Wu, Yijing Tang, Dong Zhang, Qiang Chen, Jie Zheng
Summary: The study introduces a new protein unfolding-chemical coupling (PNC) strategy to fabricate high strength, pure protein hydrogels with excellent cell biocompatibility. This method combines thermal-induced protein unfolding/gelation and -NH2/-COOH coupling reaction to achieve both physical and chemical crosslinked networks, resulting in hydrogels with high mechanical properties, transparency, stability, and low cytotoxicity. The PNC strategy can be applied to various proteins to create different high strength hydrogels, demonstrating its potential as a universal method for preparing multi-functional protein hydrogels.
Article
Multidisciplinary Sciences
Yiqun Zhang, Qi Liu, Wenjuan Ren, Yangyang Song, Hua Luo, Yangyang Han, Liang He, Xiaodong Wu, Zhuqing Wang
Summary: This study presents a new paradigm of bioinspired tactile sensors that can detect both the intensity and direction of mechanical stimulations. The sensors utilize a microcrack-bristle structure and cross-shaped configuration engineering to achieve high sensitivity and direction recognition. The as-fabricated tactile sensors demonstrate desirable stability and the ability to resolve both mechanical intensity and directional features, making them suitable for surface texture recognition and biomimetic path explorations.
Article
Engineering, Electrical & Electronic
Duncan G. Raitt, Sara-Adela Abad, Shervanthi Homer-Vanniasinkam, Helge A. Wurdemann
Summary: This paper proposes a novel optical-based soft-tipped force sensor capable of adjusting its range and sensitivity through pneumatic modulation. The sensor can reliably measure normal forces and also measure the angle and magnitude of non-normal forces.
IEEE SENSORS JOURNAL
(2022)
Article
Agriculture, Multidisciplinary
Shumao Cui, Cailing Chen, Jiayu Gu, Bingyong Mao, Hao Zhang, Jianxin Zhao, Wei Chen
Summary: The study genetically engineered Lactobacillus plantarum ST-III to express GFP and studied its distribution in the intestine of mice using fluorescence imaging. The results showed that the genetically modified strain could survive in the intestine and be detected at various time points. The fluorescence intensity was found to have a linear relationship with the viable count of the strain, suggesting that fluorescence intensity can be used to estimate the amount of the strain in the intestinal tract.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Article
Anatomy & Morphology
Nikolay A. Barinov, Elizaveta R. Pavlova, Anna P. Tolstova, Ainur G. Matveeva, Aleksandr P. Moskalets, Evgeniy Dubrovin, Dmitry Klinov
Summary: This study reports a new type of non-conventional fibrinogen clot formation mediated by myeloperoxidase, even at low concentrations. The researchers discovered that these clots have a different morphology compared to conventional fibrin clots and found that myeloperoxidase interacts directly with fibrinogen molecules, leading to the unfolding of the protein. The results provide new insights into fibrinogen clotting and open up possibilities for the development of fibrinogen-based biomaterials.
MICROSCOPY RESEARCH AND TECHNIQUE
(2022)
Article
Biochemistry & Molecular Biology
Hannah E. Chia, Karl J. Koebke, Aathmaja A. Rangarajan, Nicole M. Koropatkin, E. Neil G. Marsh, Julie S. Biteen
Summary: A novel orange UnaG-ligand pair has been identified, which can be excited in the 532 nm green excitation microscopy channel and emits at 581 nm, showing high affinity for UnaG and a significant increase in fluorescence intensity and red shift in anoxic environments. This discovery expands the versatility of UnaG ligand-binding pocket for cell imaging at longer wavelengths.
ACS CHEMICAL BIOLOGY
(2021)
Article
Engineering, Biomedical
Giuseppe Florio, Nicola M. Pugno, Markus J. Buehler, Giuseppe Puglisi
Summary: The study proposes a simple general framework to predict various aspects of protein structural analyses, focusing on global features of the proteins. The model is demonstrated to be effective in capturing the folding and unfolding behaviors of tropoelastin and its mutations. Additionally, the approach is shown to reproduce important properties of the folding-unfolding mechanical response.
ACTA BIOMATERIALIA
(2021)
Review
Chemistry, Inorganic & Nuclear
Min Qiao, Liping Ding, Fengting Lv
Summary: This paper introduces the development of fluorescent sensors for metal ions based on fluorescent ensembles, particularly focusing on the strategies for obtaining these sensors and methods for adjusting their sensing behaviors.
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Physics, Multidisciplinary
Luigi Zanovello, Michele Caraglio, Thomas Franosch, Pietro Faccioli
Summary: The study shows that active Brownian particles reach the target more frequently and follow longer and counterintuitive search patterns compared to passive Brownian particles, leading to significant changes in the structure and kinetics of the ensemble of transition paths even in a simple landscape.
PHYSICAL REVIEW LETTERS
(2021)
Article
Mechanics
Lukas Schrack, Charlotte F. Petersen, Michele Caraglio, Gerhard Jung, Thomas Franosch
Summary: In this study, the motion of tagged particles in a strongly interacting quasi-confined liquid was investigated using periodic boundary conditions. The calculations were based on mode-coupling theory of the glass transition and comparisons were made with event-driven molecular dynamics simulations. The results showed non-monotonic behavior in the in-plane mean-square displacement and correlations related to perpendicular motion.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Physics, Multidisciplinary
Felipe Barra, Karen Hovhannisyan, Alberto Imparato
Summary: This paper introduces and studies a cyclic battery-charger quantum device that is in thermal equilibrium or in a ground state during the charge storing stage. The study shows that the extracted energy and thermodynamic efficiency can be enhanced by operating the cycle close to the quantum phase transition point. The performance of the device is further optimized by leveraging the correlations between the battery and the charger.
NEW JOURNAL OF PHYSICS
(2022)
Article
Polymer Science
Giulia Amici, Michele Caraglio, Enzo Orlandini, Cristian Micheletti
Summary: In this study, catenated ring polymers confined inside channels and slits were investigated using Langevin dynamics simulations. It was found that catenation constraints generate a drag that couples the contour motion of the interlocked regions. The strength of this coupling decreases as the interlocking becomes tighter and shorter due to confinement, with the results having implications for linked biomolecules in experimental or biological confining conditions.
Editorial Material
Mechanics
A. Imparato
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Physics, Multidisciplinary
A. Pelizzola, M. Pretti
Summary: We study a totally asymmetric simple exclusion process with open boundary conditions and local resetting at the injection node. Using mean-field approximation and kinetic Monte Carlo simulations, we identify three regimes based on the scaling of the resetting rate with lattice size. The intermediate resetting regime is the most interesting, showing phase separation phenomena not possible with periodic boundary conditions. We discuss density profiles and nearest-neighbor covariances, finding agreement between mean-field and simulation results. The stationary state phase diagram is analytically mapped at the mean-field level, with conjecture of exactness in the thermodynamic limit. The large resetting regime, which exhibits a logarithmically diverging inverse characteristic length scale with lattice size, is briefly discussed.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Physics, Multidisciplinary
Michele Caraglio, Thomas Franosch
Summary: This study provides an analytical solution for the time-dependent Fokker-Planck equation of a two-dimensional active Brownian particle. By using the passive Brownian particle as basis states, the authors show that the Fokker-Planck operator becomes lower diagonal, indicating that the eigenvalues are not affected by activity. They further express the propagator as a combination of equilibrium eigenstates with exact iterative relations for the weights.
PHYSICAL REVIEW LETTERS
(2022)
Article
Mechanics
Victor S. Dotsenko, Pascal Viot, Alberto Imparato, Gleb Oshanin
Summary: We study the two-dimensional Langevin dynamics of a mixture of two types of particles with different temperatures and find that the system evolves into a peculiar non-equilibrium steady-state. The particles experience rotational motion due to the influence of a non-zero local curl, similar to spinning top toys, and show emergent cooperative behavior in the spatial components of the probability currents for the dissimilar species.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Multidisciplinary Sciences
Luigi Zanovello, Richard J. G. Loffler, Michele Caraglio, Thomas Franosch, Martin M. Hanczyc, Pietro Faccioli
Summary: Artificial cells can exhibit survival behavior similar to living organisms, responding to environmental stimuli and undertaking specific displacements. However, a clear definition and characterization of these survival strategies from a statistical physics perspective is still lacking. This study applies Transition Path Theory to active systems and demonstrates its usefulness in identifying survival strategies, improving modeling, and making experimentally testable predictions. The definition of survival in artificial systems allows for a formal characterization and prediction of complex life-like behaviors.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Artificial Intelligence
Harpreet Kaur, Thomas Franosch, Michele Caraglio
Summary: Developing behavioral policies to solve target-search problems efficiently is important in both natural and nanotechnology fields. This study characterizes the target-search strategies of microswimmers by analyzing their behavior in a homogeneous environment with unknown positions of sparse targets. The results show that microswimmers can control their dynamics by switching between different motions and adjusting the time duration of each phase. The optimal policies are found through the evolutionary pressure based on the target-search performances of single individuals using the genetic algorithm NeuroEvolution of augmenting topologies, which reveals various network topology solutions.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2023)
Article
Physics, Fluids & Plasmas
Francesco Di Trapani, Thomas Franosch, Michele Caraglio
Summary: In this paper, we solve the time-dependent Fokker-Planck equation for a two-dimensional active Brownian particle exploring a circular region with an absorbing boundary. We provide a matrix representation of the Fokker-Planck operator using the passive Brownian particle as basis states and treating the activity as a perturbation. The propagator is expressed in terms of perturbed eigenvalues and eigenfunctions or as a combination of equilibrium eigenstates with weights dependent on time and initial conditions, following exact iterative relations. Additionally, we obtain the survival probability and the first-passage time distribution, which exhibit peculiarities induced by the nonequilibrium nature of the dynamics, such as strong dependence on the particle's activity and, to a lesser extent, its rotational diffusivity.
Article
Physics, Multidisciplinary
Ricardo Puebla, Alberto Imparato, Alessio Belenchia, Mauro Paternostro
Summary: We investigate the interaction between a finite one-dimensional chain of quantum rotors and thermal baths at different temperatures. When the interaction between the rotors is made chiral, the system acts as an autonomous thermal motor, converting heat currents into nonvanishing rotational ones. This behavior is strongly pronounced when the system undergoes a quantum phase transition in the ground state. The optimal operating regime of such a quantum autonomous motor is associated with large quantum coherence and multipartite quantum correlations within the state of the system.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Physics, Multidisciplinary
Gabriele De Chiara, Alberto Imparato
Summary: We present a general quantum fluctuation theorem for the entropy production of an open quantum system coupled to multiple environments, not necessarily at equilibrium. The theorem holds for different types of master equations and confirms the thermodynamic consistency of local quantum master equations. This theorem is genuinely quantum and can be expressed in terms of a conservative Hermitian operator representing the dynamics of the system state operator and the entropy change in the baths.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Polymer Science
Joseph L. Sleiman, Robin H. Burton, Michele Caraglio, Yair Augusto Gutierrez Fosado, Davide Michieletto
Summary: Inspired by proteins, researchers find that local geometric features can predict knots and entanglements in polymers. Segments with maximum local density or writhe correlate up to 90% of the time with the shortest knotted and linked arcs. Nonlocal 3D writhe is the best geometric readout of the knot location.
Article
Physics, Multidisciplinary
Adam Hewgill, Gabriele De Chiara, Alberto Imparato
Summary: Local master equations are proven to be consistent with thermodynamics and its laws for modeling open quantum systems. The study examines the energy, heat currents, and entropy production rate of a quantum system in contact with multiple baths. The results demonstrate the validity of the second law of thermodynamics and the relationship between quantum probability currents and energy currents.
PHYSICAL REVIEW RESEARCH
(2021)
