Tyler O'Neal, Staff Editor

FSU researchers discover even small disturbances can trigger catastrophic storms

You've probably seen the satellite images that show a hurricane developing: thick white clouds clumping together, arms spinning around a central eye as it heads for the coast.

After decades of research, meteorologists still have questions about how hurricanes develop. Now, Florida State University researchers have found that even the smallest changes in atmospheric conditions could trigger a hurricane, information that will help scientists understand the processes that lead to these devastating storms.

"The whole motivation for this paper was that we still don't have that universal theoretical understanding of exactly how tropical cyclones form, and to really be able to forecast that storm-by-storm, it would help us to have that more solidly taken care of," said Jacob Carstens, a doctoral student in the Department of Earth, Ocean, and Atmospheric Science.

The research by Carstens and Assistant Professor Allison Wing has been published in the Journal of Advances in Modeling Earth Systems. This is Jacob Carstens, a doctoral student in the Department of Earth, Ocean and Atmospheric Science.

Current theories on the formation of hurricanes agree that some sort of disturbance must exist to start the process that leads to a hurricane. Carstens used numerical models that started with simple conditions to better understand exactly how those disturbances arise.

"We're trying to go as bare-bones as possible, looking at just how exactly clouds want to organize themselves without any of these external factors playing into it to form a tropical cyclone more efficiently," he said. "It's a way we can further round out our broader understanding and look more purely at the actual tropical cyclones themselves rather than the surrounding environment's impact on it."

The simulations started with mostly uniform conditions spread across the imaginary box where the model played out. Then, researchers added a tiny amount of random temperature fluctuations to kickstart the model and observed how the simulated clouds evolved. {module INSIDE STORY}

Despite the random start to the simulation, the clouds didn't stay randomly arranged. They formed into clusters as the water vapor, thermal radiation and other factors interacted. As the clusters circulated through the simulated atmosphere, the researchers tracked when they formed hurricanes. They repeated the model at simulated latitudes between 0.1 degrees and 20 degrees north, representative of areas such as parts of western Africa, northern South America, and the Caribbean. That range includes the latitudes where tropical cyclones typically form, along with latitudes very close to the equator where their formation is rare and less studied.

The scientists found that every simulation in latitudes between 10 and 20 degrees produced a major hurricane, even from the stable conditions under which they began the simulation. These came a few days after a vortex first emerged well above the surface and affected its surrounding environment.

They also showed the possibility of cloud interaction contributing to the development of a tropical cyclone very close to the equator, which rarely occurs in nature but has still been observed as close as 1.4 degrees north away.

Hurricanes are dangerous weather events. Forecasting can help prevent deaths, but a big storm can still cause billions of dollars in damage. A better theoretical understanding of their formation will help meteorologists predict and prepare for these storms, both in short-term forecasts and long-term climate projections and communicate their understanding to the public.

"It's becoming ever more important in our field that we connect with emergency managers, the general population and other local officials to advise them on what they can expect, how they should prepare and what sorts of impacts are going to be heading their way," Carstens said. "A more robust understanding of how tropical cyclones form can help us to better forecast their location, their track, and their intensity. It really goes down the line and helps us to communicate sooner as well as more efficiently and eloquently to the public that really needs it."

Russian supercomputer modeling reveals behavior of individual lipid molecules

Tyler O'Neal, Staff Editor

Lipids are essential building blocks of cell membranes, which control the exchange of substances and energy between a cell and its environment. Developed at the Moscow Institute of Physics and Technology, a new open-source software tool PCAlipids aims to analyze lipid behavior. The new program has been presented in a paper that comes out in print in the upcoming July 1 issue of Biochimica et Biophysica Acta -- Biomembranes.

Every living cell is surrounded by a membrane that serves a number of vital functions, from facilitating the uptake of materials essential for survival to controlling cell regulatory processes. What enables this wide range of functions is the unique structure of the membrane: almost rigid proteins incorporated in a flexible lipidic layer. CAPTION Lipids are essential building blocks of cell membranes, which control the exchange of substances and energy between a cell and its environment. Developed at the Moscow Institute of Physics and Technology, a new open-source software tool PCAlipids aims to analyze lipid behavior. CREDIT Daria Sokol/MIPT Press Office{module INSIDE STORY}

The lipid composition of membranes has been found to influence how the individual proteins and the membrane as a whole function, therefore emphasizing the importance of lipids. However, the exact molecular mechanism of lipid-protein interplay is yet to be uncovered. PCAlipids is an important step toward understanding that mechanism.

Ways to examine lipid-protein interplay in membranes

The studies of membrane proteins and lipids cannot rely on the same techniques. While a host of experimental methods are available to study protein functioning, they lack either temporal or spatial resolution for analyzing lipids. To close this gap, various computational techniques are employed.

One of them, molecular dynamics simulations, enable researchers to examine the dynamics of a molecular system with atomic precision and at a timescale of picoseconds, or trillionths of a second. In order to achieve biologically relevant temporal and spatial scales, the interatomic interactions of quantum nature are simplified to classical representation. The method involves calculating the forces that act on each atom and solving the associated Newton's equations of motion. The set of parameters used to define interatomic forces is called a force field.

To make sure that force fields are reliable, they undergo validation: Simulation results are contrasted with actual experimental data. The force fields used to model the behavior of the protein-lipid systems in cell membranes require such validation, too. That defines the focus of the tools that aim to analyze the simulations of membrane systems: It is mainly the experimentally measurable quantities that are extracted from the simulations. Due to the limitations of experimental techniques, the currently used analyses focus on large groups of lipids, while the behavior of individual lipids does not get much attention.

New software to analyze individual lipids

Pavel Buslaev, Khalid Mustafin, and Ivan Gushchin from the MIPT Research Center for Molecular Mechanisms of Aging and Age-Related Diseases have developed an open-source script called PCAlipids that analyzes the structure of individual lipid molecules at a given moment and describes their conformational changes -- the reshaping of molecules. A method known as principal component analysis underlies the script.

"PCAlipids is a piece of software that enables describing the motion of an individual molecule. While our study focused on lipids, the method is applicable to other molecules as well," explained Buslaev, who is a researcher at the MIPT Laboratory of Structural Analysis and Engineering of Membrane Systems.

"As of now, it is not possible to experimentally measure the values analyzed by PCAlipids," he added. "However, we have proposed several experiments. Hopefully, this will lead to the development of a new experimental area. The resulting data could then be contrasted with simulated lipid behavior to refine model parameters."

PCAlipids first identifies groups of atoms moving together. Next, it defines a new basis, such that the first basis vector is associated with the collective motion that has the largest amplitude and involves the largest number of atoms. The second most important motion determines the second basis vector and so on.

The analysis that follows relies on the established basis and aims to determine the effects of various factors on the lipid molecules. For example, an additional compound can be introduced into the simulation. If that affects the first, most significant collective motions, it means the compound will have a major influence on the membrane. Otherwise, its impact will below. The manner in which the collective motions are impacted can reveal the mechanisms behind the compound's effects.

Effects of temperature, cholesterol, and more on lipids

The team from MIPT used the new software to study the effects of temperature, cholesterol, and membrane curvature on individual lipids. These parameters have long been known to influence the behavior of the membrane as a whole, but it remained unknown how they affect individual molecules.

Lowering the temperature causes the membrane to undergo a phase transition: The lipids become largely ordered. PCAlipids helped to highlight the beginning of phase transition and quantitatively describe how the number of possible lipid structures varies as the freezing point is approached. It turned out that this number remains stable up until freezing, but the rate of transitions between these structures grows progressively slower.

Cholesterol is a crucial cell membrane component that promotes lipid order. PCAlipids revealed that significant collective motions become more compact in the presence of cholesterol. The simulation also exposed the mechanism that mediates the effects of cholesterol on lipid order.

The cell membrane is flexible and tends to bend a lot, which is vital to its functioning. This leads to one membrane layer being convex and the other concave. Both configurations proved to accommodate the same range of possible lipid structures; however, the rate of transitions between different structures is noticeably higher in the convex layer.

The study has demonstrated that PCAlipids can be used to investigate the structure of lipid systems. The tool replicates the findings of prior research but also reveals details that remained elusive up until now. This illustrates the potential of the new software developed at MIPT to provide insights into the processes that occur in cell membranes.

Where, when will oil spills reach the beach?

Tyler O'Neal, Staff Editor

In October 2018, the Tunisian Ro-Ro passenger ship "Ulysse" rammed into the hull of the Cyprus-flagged container ship "Virginia", which was anchored in international waters off the northern tip of Corsica, an area known for its pristine waters and beaches. Bunker fuel from Virginia leaked out of her tanks through a breach several meters long, threatening the marine environment and coastal areas. 530 m3 of oil was released, and in 36 hours the slick had lengthened to cover approximately 35 km.

Predicting the drift of oil slicks on water surfaces and in coastal zones is fundamental for responding to spill events and to mitigate their impacts on the environment, allowing for more efficient use of emergency response resources.

A recently published scientific paper tells about the collaboration that was formed for this purpose, between the researchers of the CMCC Foundation - Euro-Mediterranean Center on Climate Change and REMPEC, the Regional Marine Pollution Emergency Response Centre for the Mediterranean Sea, based in Malta, right after the collision of Ulysse with Virginia. CAPTION Pink polygons indicate the area where the model was restarted from on 10 Oct. 2018. A blue cross marks the ships' point collision. CREDIT ©Svitlana Liubartseva, CMCC Foundation{module INSIDE STORY}

"Thanks to a joint effort involving an efficient and timely exchange of information, we received observational data from REMPEC and used these real observations as the starting point for our model in order to calculate the forecast", explains Svitlana Liubartseva, a researcher at the CMCC Foundation and first author of the study. "We worked day and night, and provided REMPEC with 5 forecast bulletins during the oil spill tracking and recovery operations."

Forecast of currents, wind, waves and sea surface temperatures are critical for predicting the spread and fate of oil. The study is focused on the ability to realistically predict the times and places where oil reaches coastlines thanks to the oceanographic model MEDSLIK-II, developed by CMCC Foundation. The model results were verified by comparing available observational data.

"Using the oceanographic and atmospheric dataset provided by the Copernicus Marine Environment Monitoring Service (CMEMS) and the European Centre for Medium-Range Weather Forecasts (ECMWF) we produced forecasts of the oil drift. The CMEMS output has a high resolution of about 4 km, that allowed us to produce a rather good quality of prediction of when and where the oil reached the beaches", specifies Dr. Liubartseva.

For the first 16 days after the accident, the model was able to generate reliable predictions, forecasting the oil movements at least 7 days in advance. Researchers were able to predict almost precisely the place and time where the oil would reach the coast for the first time. After more than 9 days drifting at sea, it landed near Saint-Tropez (France). Due to a lack of observational data, in the long run, there was a deterioration in the model solution, as the oil drifted for about one month. Nevertheless, the research demonstrates that the CMCC model facilitates the use and optimization of anti-pollution resource deployment and increases coastal preparedness.

CMCC researchers are now at work to further improve the predictability of oil spill drift and transformation. On the one hand, there is the need to improve the resolution of the models, making their grid finer and finer, which will involve studying more oil spill events to get better predictions.