Machine Learning for Molecular dynamics — Why bother?
Chalmers University of Technology
20 October 2021
With faster compute-infrastructures, molecular simulations play an increasingly important role in the basic sciences and application areas such as drug and materials design. Simultaneously, machine learning and artificial intelligence are receiving increased attention due to increasing volumes of data generated both inside and outside of science. In this talk, I will talk about a few applications of these technologies in molecular simulation, focusing on biomolecular simulations [1,2]
 Olsson & Noé ”Dynamic Graphical Models of Molecular Kinetics” Proc. Natl. Acad. Sci. U.S.A. (2019) doi: 10.1073/pnas.1901692116.
 Noe†, Olsson, Köhler, Wu ”Boltzmann Generators: Sampling Equilibrium States of Many-Body Systems with Deep Learning” Science (2019). 365, eaaw1147. doi:10.1126/science.aaw1147.
The study, recently published in Biophysics Reviews, shows how artificial intelligence can be used to develop faster, cheaper and more reliable information about cells, while also eliminating the disadvantages from using chemicals in the process.
Thomas Suphona defended his Master thesis in Physics at the Chalmers University of Technology on 27 september 2021. Congrats!
Title: Collective behaviors of autonomous robots in complex environment
Collective behaviours or collective motion is a common phenomena in nature where multiple organisms in a system undergo ordered movements. This can be observed in different scales, from the microscale with bacteria swarming to the macro scale with for example flocks of birds, schools of fish and even human crowds and car traffic.
All these systems are made up by self-propelling agents who are able to take up energy from their environment and converting it to directed motion.
Because of this
property of self-propulsion, their dynamics cannot be explained using conventional methods. Although significant efforts have been made in trying to explain collective behaviours from different perspective, using simulation tools and study systems in different scales as mentioned before, the subject is not as widely studied from the macroscale, especially with artificially made systems. In this thesis, a macroscale system was design with the purpose of providing conditions for collective behaviours to emerge and study how the behaviours changes depending on the surrounding conditions. Battery powered robots were used as self-propelling agents and they were placed in a confined space filled with obstacles. It was shown that when the number of robot and obstacles inside the system is large, the robots movements were significantly restricted. The weight of the obstacles do also affect the average motions of the robots where heavier obstacles hinders the robots by creating blockage leading to the robots having lower average velocity. At certain configuration of the parameters, the robots showed collective behaviours where they for example form channels between the obstacles, making ”roads” for other robots to reuse, or helping each other to move by pushing away chunks of obstacles or pushing onto each other. Even though these robots are simple agents, they have manage to manifest cooperative actions towards other agents.
Supervisor: Giovanni Volpe and Alessandro Magazzú Examiner: Giovanni Volpe Opponent: David Fitzek
Machine Learning for Active Matter: Opportunities and Challenges
(online at) ICTP, Trieste, Italy
8 September 2021, 11:30 CEST
Machine-learning methods are starting to shape active-matter research. Which new trends will this start? Which new groundbreaking insight and applications can we expect? More fundamentally, what can this contribute to our understanding of active matter? Can this help us to identify unifying principles and systematise active matter? This presentation addresses some of these questions with some concrete examples, exploring how machine learning is steering active matter towards new directions, offering unprecedented opportunities and posing practical and fundamental challenges. I will illustrate some most successful recent applications of machine learning to active matter with a slight bias towards work done in my research group: enhancing data acquisition and analysis; providing new data-driven models; improving navigation and search strategies; offering insight into the emergent dynamics of active matter in crowded and complex environments. I will discuss the opportunities and challenges that are emerging: implementing feedback control; uncovering underlying principles to systematise active matter; understanding the behaviour, organisation and evolution of biological active matter; realising active matter with embodied intelligence. Finally, I will highlight how active matter and machine learning can work together for mutual benefit.
Barbora Spackova joins the Soft Matter Lab at the Physics Department of the University of Gothenburg on 1st September 2021.
Barbora has a PhD in physical engineering from the Czech Technical University in Prague (Czech Republic). Formerly, she has been a researcher at Chalmers University of Technology in the group of Prof. Christoph Langhammer. Her research is focused on single-molecule detection in nanofluidic systems.
While part of the Soft Matter Lab, she will continue her research on characterising cell media containing exosomes using Nanofluidic Scattering Microscopy (NSM).
The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus
Karla C. Hernández Ramos, Edna Rodríguez-Sánchez, Juan Antonio Arias del Angel, Alejandro V. Arzola, Mariana Benítez, Ana E. Escalante, Alessio Franci, Giovanni Volpe, Natsuko Rivera-Yoshida
Sci. Adv. 7(35), eabh2278 (2021)
The social soil-dwelling bacteria Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physico-chemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus. In topographies realized by randomly placing silica particles over agar plates, we observe that the cells’ interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size and shape of the fruiting bodies, and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a minimal computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological and medical relevance.
The Cognitive Connectome in Healthy Aging
Eloy Garcia-Cabello, Lissett Gonzalez-Burgos, Joana B. Pereira, Juan Andres Hernández-Cabrera, Eric Westman, Giovanni Volpe, José Barroso, & Daniel Ferreira
Front. Aging Neurosci. 13, 530 (2021)
Objectives: Cognitive aging has been extensively investigated using both univariate and multivariate analyses. Sophisticated multivariate approaches such as graph theory could potentially capture unknown complex associations between multiple cognitive variables. The aim of this study was to assess whether cognition is organized into a structure that could be called the “cognitive connectome,” and whether such connectome differs between age groups.
Methods: A total of 334 cognitively unimpaired individuals were stratified into early-middle-age (37–50 years, n = 110), late-middle-age (51–64 years, n = 106), and elderly (65–78 years, n = 118) groups. We built cognitive networks from 47 cognitive variables for each age group using graph theory and compared the groups using different global and nodal graph measures.
Results: We identified a cognitive connectome characterized by five modules: verbal memory, visual memory—visuospatial abilities, procedural memory, executive—premotor functions, and processing speed. The elderly group showed reduced transitivity and average strength as well as increased global efficiency compared with the early-middle-age group. The late-middle-age group showed reduced global and local efficiency and modularity compared with the early-middle-age group. Nodal analyses showed the important role of executive functions and processing speed in explaining the differences between age groups.
Conclusions: We identified a cognitive connectome that is rather stable during aging in cognitively healthy individuals, with the observed differences highlighting the important role of executive functions and processing speed. We translated the connectome concept from the neuroimaging field to cognitive data, demonstrating its potential to advance our understanding of the complexity of cognitive aging.
Enhanced prediction of atrial fibrillation and mortality among patients with congenital heart disease using nationwide register based medical hospital data and neural networks
Kok Wai Giang, Saga Helgadottir, Mikael Dellborg, Giovanni Volpe, Zacharias Mandalenakis
European Heart Journal – Digital Health (2021)
Aims: To improve short-and long-term predictions of mortality and atrial fibrillation (AF) among patients with congenital heart disease (CHD) from a nationwide population using neural networks (NN).
Methods and results: The Swedish National Patient Register and the Cause of Death Register were used to identify all patients with CHD born from 1970 to 2017. A total of 71 941 CHD patients were identified and followed-up from birth until the event or end of study in 2017. Based on data from a nationwide population, a NN model was obtained to predict mortality and AF. Logistic regression (LR) based on the same data was used as a baseline comparison. Of 71 941 CHD patients, a total of 5768 died (8.02%) and 995 (1.38%) developed AF over time with a mean follow-up time of 16.47 years (standard deviation 12.73 years). The performance of NN models in predicting the mortality and AF was higher than the performance of LR regardless of the complexity of the disease, with an average area under the receiver operating characteristic of >0.80 and >0.70, respectively. The largest differences were observed in mortality and complexity of CHD over time.
Conclusion: We found that NN can be used to predict mortality and AF on a nationwide scale using data that are easily obtainable by clinicians. In addition, NN showed a high performance overall and, in most cases, with better performance for prediction as compared with more traditional regression methods.