Article
Multidisciplinary Sciences
Nicolas Waisbord, Amin Dehkharghani, Jeffrey S. Guasto
Summary: Through microfluidic experiments, it was found that individual magnetotactic bacteria display three distinct regimes when directed upstream through pores, resembling the electrical conductivity of a diode. This diode-like behavior persists at the pore scale, impacting flow conductivity in higher dimensional geometries. The study has implications for magnetotactic bacteria survival strategies in sediments and potential drug delivery applications in vascular networks.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Miru Lee, Christoph Lohrmann, Kai Szuttor, Harold Auradou, Christian Holm
Summary: The study focuses on the transport of bacteria in a porous media modeled by a square channel with a cylindrical obstacle, using molecular dynamics simulations and lattice Boltzmann fluid. By varying the external flow strength, bacterial motility, and channel geometry, the research reveals the crucial interactions between bacteria and confining walls for the accumulation process.
Article
Multidisciplinary Sciences
Jyot D. Antani, Rachit Gupta, Annie H. Lee, Kathy Y. Rhee, Michael D. Manson, Pushkar P. Lele
Summary: The bacterial flagellar motor is able to adapt its switching between clockwise and counterclockwise rotation in response to changes in mechanical load by controlling the binding affinity of the chemotaxis response regulator, CheY-P. This allows the motor to maintain optimal function in environments of varying viscosities. The interplay between mechanical forces and CheY-P binding tunes the chemotactic function to match the load, resembling proprioceptive feedback in neuromuscular systems.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
Remy Colin, Bin Ni, Leanid Laganenka, Victor Sourjik
Summary: Swimming bacteria can follow gradients of nutrients and signaling molecules for optimal growth, with chemotaxis enhancing efficiency in environmental colonization. The balance between individual and collective behaviors is crucial, with multiple roles of motility and chemotaxis in bacterial swarming, biofilm formation, and interactions with hosts.
FEMS MICROBIOLOGY REVIEWS
(2021)
Article
Microbiology
Sooyeon Song, Thomas K. Wood
Summary: AI-2, a ubiquitous metabolite, has been shown to influence biofilm formation and motility in Escherichia coli, establishing it as a true signal with important physiological roles. Additionally, AI-2 signaling in E. coli is compared to indole signaling, showing opposite effects on biofilm formation and virulence.
Article
Physics, Multidisciplinary
Oleksandr Chepizhko, Thomas Franosch
Summary: This study investigates the dynamics of a single chiral active particle under an external torque caused by the presence of a gravitational field. Through computer simulations, it is observed that the longtime diffusivity of the gravitactic agent significantly increases when the external torque approaches the intrinsic angular drift. Analytic expressions for the mean-square displacement are provided using eigenfunctions and eigenvalues of the noisy-driven-pendulum problem. The pronounced maximum in the diffusivity is explained by the vanishing of the lowest eigenvalues of the Fokker-Planck equation for the angular motion as the rotational diffusion decreases and the underlying classical bifurcation is approached. A simple harmonic oscillator model accurately describes the onset of resonance during barrier-dominated motion.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biophysics
Margaritis Voliotis, Jerko Rosko, Teuta Pilizota, Tanniemola B. Liverpool
Summary: This study establishes a link between the measured steady-state switching rates of the flagellar rotary system and the directional changes of individual swimming bacteria in a gradient, using a probabilistic model. The complex response of a bacterial population to the gradient suggests that both the average speed and distribution width of the response should be considered when optimizing the overall population's performance in complex environments.
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Fluids & Plasmas
Mohammad Nabil, Andrew Frankowski, Ashton Orosa, Andrew Fuller, Amir Nourhani
Summary: We proposed a method to modulate the drifting motion of overdamped circle swimmers in steady fluid flows by static sinusoidal potentials, and quantified the drift velocity as a function of potential strength and wavelength with and without diffusional motion. The results show that drift velocity is essentially quantized without diffusion but has a continuous range with noise, and different regimes can be observed based on the dimensionless potential wave number in the drift velocity diagram. This method can help differentiate biological and artificial circle swimmers based on their dynamical properties.
Article
Multidisciplinary Sciences
Hiroto Tanaka, Yasuaki Kazuta, Yasushi Naruse, Yukihiro Tominari, Hiroaki Umehara, Yoshiyuki Sowa, Takashi Sagawa, Kazuhiro Oiwa, Masato Okada, Ikuro Kawagishi, Hiroaki Kojima
Summary: Chemical sensing is crucial for the survival of organisms. Bacterial chemotaxis regulates flagellar rotation direction based on chemical signals, and can determine the favorability of chemicals. An experimental setup and statistical framework were used to monitor and extract information on chemical stimuli from the responses of bacteria. This research provides a basis for developing novel bio-inspired sensors to detect a wider range of chemicals.
SCIENTIFIC REPORTS
(2022)
Review
Physics, Applied
Oskar Hallatschek, Sujit S. Datta, Knut Drescher, Joern Dunkel, Jens Elgeti, Bartek Waclaw, Ned S. Wingreen
Summary: The fascinating patterns of collective motion created by autonomously driven particles have fueled active-matter research for over two decades. In this Perspective, researchers argue that the unique features emerging in systems with proliferation represent a distinct form of activity, and propose proliferation as another direction of active-matter physics. They believe that by extending the conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics.
NATURE REVIEWS PHYSICS
(2023)
Article
Multidisciplinary Sciences
Mariia Dvoriashyna, Eric Lauga
Summary: E. coli bacteria swim by rotating helical flagellar filaments, moving steadily forward during 'runs' and undergoing erratic motion and reorientation during 'tumble' events. Alternating between runs and tumbles allows cells to stochastically change their propulsion direction. The change in direction during a tumble is skewed towards smaller angles.
Article
Chemistry, Physical
Longfei Li, Wenjian Li, Ke Chen, Ning Zheng, Mingcheng Yang
Summary: This study focuses on the migration behavior of active colloidal cells (ACCs) on a substrate with mechanical inhomogeneities. The ACCs can migrate unidirectionally across the interface of a heterogeneous environment and exhibit tactical behavior, which is qualitatively different from the behavior of the constituent active particles themselves. The findings provide insights into understanding the taxis of biological cells and designing biomimetic cells with environment-sensitive capabilities.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemical Research Methods
Liliana Angeles-Martinez, Vassily Hatzimanikatis
Summary: This study analyzes the sensitivity of biofilm simulation to crowding conditions and finds that traditional methods may not accurately capture the diverse nature of biofilms. The modeling of crowding conditions in microbial systems can guide the selection of effective treatments for disrupting and controlling biofilms associated with chronic diseases.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Elena Sese-Sansa, Demian Levis, Ignacio Pagonabarraga
Summary: This article discusses a dynamical field theory for self-propelled particles subjected to generic torques and forces. By coarse-graining their microscopic dynamics, the study investigates the instabilities of macroscopic and finite structures, and the influence of intrinsic torques on phase separation and non-equilibrium patterns.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Helena Massana-Cid, Claudio Maggi, Giacomo Frangipane, Roberto Di Leonardo
Summary: Optical feedback can be used to confine and gather bacteria, forming dense high-activity regions. This method is general and scalable, making it versatile for microengineering applications and studying non-equilibrium phenomena in active systems.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Fluids & Plasmas
V. Jemseena, Manoj Gopalakrishnan
Article
Chemistry, Physical
Deepak Bhat, Manoj Gopalakrishnan
EUROPEAN PHYSICAL JOURNAL E
(2016)
Article
Physics, Multidisciplinary
Deepak Bhat, Manoj Gopalakrishnan
Article
Biology
P. K. Jithinraj, Ushasi Roy, Manoj Gopalakrishnan
JOURNAL OF THEORETICAL BIOLOGY
(2014)
Correction
Biology
P. K. Jithinraj, Ushasi Roy, Manoj Gopalakrishnan
JOURNAL OF THEORETICAL BIOLOGY
(2014)
Correction
Biology
P. K. Jithinraj, Ushasi Roy, Manoj Gopalakrishnan
JOURNAL OF THEORETICAL BIOLOGY
(2014)
Article
Physics, Fluids & Plasmas
V. Jemseena, Manoj Gopalakrishnan
Article
Physics, Multidisciplinary
C. S. Renadheer, Ushasi Roy, Manoj Gopalakrishnan
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2019)
Article
Biochemistry & Molecular Biology
Vandana Yadav, Balaramamahanti Srinivas, Manoj Gopalakrishnan
Summary: This study investigates the impact of barriers on the dynamics of microtubule filaments in cells and the extent of load-sharing in a microtubule bundle, analyzing their effects on catastrophe events. Theoretical models and numerical simulations are used to study the dynamic behavior and interactions between microtubules and barriers in different scenarios.
Article
Physics, Multidisciplinary
Urvashi Nakul, Manoj Gopalakrishnan
Summary: This study investigates the phenomenon of protein friction in transporting cellular cargoes along the cytoskeletal filament track. Through mathematical modeling and computational simulations, the motion of motor proteins and the related drag coefficient are analyzed. Results show the relationship between motor protein friction and background damping force, as well as the behavior when multiple motors are involved in transportation.
Article
Chemistry, Physical
Vandana Yadav, Manoj Gopalakrishnan
Summary: The study focuses on the velocity-force relation for a Brownian ratchet in extreme limits of fast and slow barrier diffusion, deriving different V-F relations and the impact of filament number on velocity. Mean-field argument predicts equal load sharing in both limits, but different scaling behavior of velocity with filament number.
EUROPEAN PHYSICAL JOURNAL E
(2022)
Article
Biochemistry & Molecular Biology
Srestha Roy, Rahul Vaippully, Muruga Lokesh, Gokul Nalupurackal, Vandana Yadav, Snigdhadev Chakraborty, Manoj Gopalakrishnan, Privita Edwina Rayappan George Edwin, Saumendra Kumar Bajpai, Basudev Roy
Summary: Conventionally, only normal cell membrane fluctuations have been studied to determine membrane properties. However, a new concept called membrane local slope fluctuations has been introduced and found to behave differently than normal fluctuations. In this study, we investigate the effect of the drug Latrunculin-B on membrane fluctuations and find that while the normal fluctuations show a power law behavior, the slope fluctuations remain constant. This provides a convenient opportunity to study membrane parameters as the membrane softens after drug application. We also explore the active athermal fluctuations in the membrane and find their timescales to be slower than 1 second.
Article
Biochemistry & Molecular Biology
Balaramamahanti Srinivas, Manoj Gopalakrishnan
Proceedings Paper
Physics, Applied
Deepak Bhat, Manoj Gopalakrishnan
SOLID STATE PHYSICS, VOL 57
(2013)