Delivering Sub-Microsecond Accurate Time to Linux Applications Around the World

Total Page:16

File Type:pdf, Size:1020Kb

Delivering Sub-Microsecond Accurate Time to Linux Applications Around the World WHITE PAPER Delivering Sub-Microsecond Accurate Time to Linux Applications Around the World Time Where It’s Needed .......................1 Accurate Time Where It’s Needed of delay, making adjusting for the delay Time Offsets, Delays And Delay While the science of timekeeping has more difficult. In fact, these delays are the Variations…No Way Around Them! .......1 fascinated many over the years, what primary source of time transfer error. In The Four Sources Of Sub-Microsecond counts most today is delivering accurate time synchronization we rely on accurately Time Error .............................................2 time to where it’s needed. If a person needs measuring timing packet transit delays to Network Path Delay Related Errors ....2 the time they may look at their phone to adjust the clocks to compute the correct time. Linux Stack Delay Related Errors ......3 Linux Clock Call Delay Errors ............3 see an accurate time that is distributed As the need for more accurate time at Clock Instability Errors ......................4 through the mobile network. If an a program increases, the impact that Solving The Sources Of Time application program running on a computer Synchronization Error ...........................5 needs the time it may execute a command variable packet delays have on the ability PTP Hardware/Software that accesses the system clock. That to correct a clock increases as well. To Combinations .......................................5 application is a consumer of the time and make matters worse, the quality of a clock Why Hardware Based PTP Slaves not a clock. Ultimately, it is the accuracy also effects how well you can synchronize Deliver The Best Timing .......................5 and precision of the time delivered to the the time. Understanding the problems and Solving Network Path Delay application program that matters most. how to compensate for them greatly helps Related Errors .......................................5 The more accurate and precise the time in delivering accurate and precise time More Packets For Better Filtering ...5 requirement is, the harder it is to deliver it. to clocks and ultimately to an application OCXO Oscillator Provides A Stable program. Time Base .......................................5 This whitepaper explores the challenges in delivering sub-microsecond accurate time Hardware Time Stamping Improves The difference between the times on to a Linux program, and it will present IEEE Time Accuracy ................................6 two clocks is known as the offset. In 1588 Precise Time Protocol (PTP) solutions Validating Synchronization Over The timekeeping we strive to keep the offset Network ..........................................6 and test data showing how to overcome below a particular value so that we can Push Time To Memory To Improve those challenges. Speed And Accuracy ...........................6 assign an accuracy value to the time on Verifying High Availability DMA Time Time Offsets, Delays and Delay the clock. Generally in synchronization Writes .............................................7 Variations…No Way Around Them! schemes one clock is more accurate than Verifying DMA Time Stamp Our objective is to deliver accurate and the other so the offset is tracked relative Accuracy .........................................7 precise time over a packet based network to the more accurate clock. Best Possible Time To Utc At to a computer, then on to the application The Application Layer ....................8 The process of setting one clock to another programs that need it. Timing packets is a matter of exchanging timing packets, Best Possible Time Around The on a network can be delayed, thereby World ..............................................9 computing the offset between a master impairing the ability to accurately transfer Conclusion, PTP Clock Cards Deliver clock and a slave clock, and making an time from one clock to another. There are The Best Possible Time Accuracy .........9 adjustment to the slave clock (called factors that cause the delays change, so clock steering when done periodically). there will also be variations in the amount Page 1 of 9 WHITE PAPER Delivering Sub-Microsecond Accurate Time to Linux Applications Around the World The time the packets take to travel from the master clock to the slave is called delay, Master Slave Time Time or path delay. Figure 1 shows the PTP packet exchanges and Equation 1 is the Timestamps fundamental offset equation the slave will known by slave use to compute the time offset and correct the time. t1 Sync Slave Time Offset= (t2-t1 )+(t3-t4) 2 t2 t1, t2 Equation 1: Determination of clock error at the slave derived from PTP message departure and arrival timestamps. The Four Sources of Sub-Microsecond t3 t1, t2, t3 Time Error Delay_Req There are four main sources of error in delivering time to an application program over a network from a master clock. t4 Asymmetric time transfer delays between the master clock and the program on the slave computer requesting the time Delay_Resp accounts for three of them. The fourth is clock instability at the slave computer t1, t2, t3, t4 (assuming the master is the more stable time source). With sub-microsecond accurate time required at an application program on a slave computer, oscillator drift and even a slight temperature change . Figure 1: Sequence diagram showing the timing event packet exchange between a PTP master clock caused by the slave computer fan can . throw the time off by several microseconds. and a PTP slave clock. Network Path Delay Related Errors In packet based networks, timing packets are exchanged between the master clock and the slave clock for the purpose of computing the time offset at the slave. If the packet exchanges were instantaneous there would be no delay and the offset Master Slave could be computed perfectly. If the packet Sync Messages Sync Messages exchange delay on the master-to-slave Network Sent on Time Delay Arrive with Varible Delays path and slave-to-master paths were identical; the offset could be easily and precisely computed since the delays would cancel each other mathematically. The Time Offset Between Clocks case where path delay is the same both ways between master and slave is called symmetric delay, and time transfer over . Figure 2: Timing messages sent from the master to the slave (and vice versa) can experience packet networks most often assumes . variable delays caused by switches in the network and application delays leading to timing errors . symmetric delay. at the slave clock. Page 2 of 9 WHITE PAPER Delivering Sub-Microsecond Accurate Time to Linux Applications Around the World Unfortunately, path delay is different Switch between master-to-slave and slave- to-master, and this difference is called Data Traffic asymmetric delay. Furthermore, not only is the delay different along the two paths, but the delay difference can also vary with each packet sent. As illustrated in Timing Traffic Figure 2, Asymmetric path delays are the main problem in accurate and precise . Figure 3: Packet queuing inside the switch where data and timing packets must be forwarded time synchronization using packet based . to the same port can introduce Packet Delay Variation (PDV) leading to timing errors. techniques over a network. In a simplified network, asymmetric delay adds a time offset error equal to one half the difference in delay times. For example, receive ports, in which case there will be Linux Stack Delay Related Errors if it took one second for the timing packet to a delay in forwarding the packets. The As timing packets exit the network they go from the master to the slave and three time the packet is delayed is called the enter the Linux stack of either the master seconds on the reverse path, the offset residence time. See Figure 3. or slave computer. While a computer may computed by the slave would be incorrect be very fast at delivering timing packets by one second. Apply this to computer Due to the variable queuing delays inside quickly to the clock steering program, any hardware that is time stamping packets the switch the timing packets exchanged delivery time variation in microseconds being exchanged every second between a between the master and slave are delayed directly adds microseconds of time master and a slave with the master having and the length of the delay is variable. synchronization error. This is because it 50 nanosecond timestamp accuracy. (That This variable delay is called Packet Delay likely introduces an asymmetric path delay. is, a PTP grandmaster with accuracy to Variation (PDV). PDV refers to the arrival Note that delays delivering a received UTC or Coordinated Universal Time—such time jitter for timing packets that are sent packet to the timing program are just as a master clock with a GPS reference.) from the master or slave to the other as critical as delays in sending timing These timing packets transit a LAN but have variable arrival times at the packets out of the computer. Differences containing switches (or worse, routers) that destination. In the world of microsecond in these stack transit times directly may add asymmetric path delay in the 10s and sub-microsecond time synchronization affect how accurately and precisely the of microseconds, which result in similar over packet networks, PDV makes it very time can be corrected, particularly in size time offset computation errors. difficult to accurately compute precise computers targeting sub-microsecond offsets and adjust the slave clock. synchronization. In other words, the Queuing and delays inside network Linux stack is another place that delay Network time protocols, such as NTP and switches are generally the culprit in packet asymmetry can occur. delays. Switches are often store-and- PTP can compensate for packet delay, forward devices. Packets received on one but only if the delay is the same in each Linux Clock Call Delay Errors port are stored temporarily while the device direction. This is why the error is referred Recall that the fundamental objective is figures out which forwarding port(s) to send to as delay asymmetry error.
Recommended publications
  • C:\Data\My Files\WP\PTTI\Proceedings TOC For
    34th Annual Precise Time and Time Interval (PTTI) Meeting TIMEKEEPING AND TIME DISSEMINATION IN A DISTRIBUTED SPACE-BASED CLOCK ENSEMBLE S. Francis Zeta Associates Incorporated B. Ramsey and S. Stein Timing Solutions Corporation J. Leitner, M. Moreau, and R. Burns NASA Goddard Space Flight Center R. A. Nelson Satellite Engineering Research Corporation T. R. Bartholomew Northrop Grumman TASC A. Gifford National Institute of Standards and Technology Abstract This paper examines the timekeeping environments of several orbital and aircraft flight scenarios for application to the next generation architecture of positioning, navigation, timing, and communications. The model for timekeeping and time dissemination is illustrated by clocks onboard the International Space Station, a Molniya satellite, and a geostationary satellite. A mathematical simulator has been formulated to model aircraft flight test and satellite scenarios. In addition, a time transfer simulator integrated into the Formation Flying Testbed at the NASA Goddard Space Flight Center is being developed. Real-time hardware performance parameters, environmental factors, orbital perturbations, and the effects of special and general relativity are modeled in this simulator for the testing and evaluation of timekeeping and time dissemination algorithms. 1. INTRODUCTION Timekeeping and time dissemination among laboratories is routinely achieved at a level of a few nanoseconds at the present time and may be achievable with a precision of a few picoseconds within the next decade. The techniques for the comparison of clocks in laboratory environments have been well established. However, the extension of these techniques to mobile platforms and clocks in space will require more complex considerations. A central theme of this paper – and one that we think should receive the attention of the PTTI community – is the fact that normal, everyday platform dynamics can have a measurable effect on clocks that fly or ride on those platforms.
    [Show full text]
  • Chapter 7. Relativistic Effects
    Chapter 7. Relativistic Effects 7.1 Introduction This chapter details an investigation into relativistic effects that could cause clock errors and therefore position errors in clock coasting mode. The chapter begins with a description of relativistic corrections that are already taken into account for the GPS satellites. Though these corrections are known and implemented [ICD-GPS-200, 1991], no similar corrections are made for GPS receivers that are in motion. Deines derived a set of missing relativity terms for GPS receivers [Deines, 1992], and these are considered in great detail here. A MATLAB simulation was used to predict the relativity effects based on the derivation of Deines, and flight data were used to determine if these effects were present. 7.2 Relativistic Corrections for the GPS Satellite The first effect considered stems from a Lorentz transformation for inertial reference frames. This effect from special relativity is derived from the postulate that the speed of light is constant in all inertial reference frames [Lorentz et. al., 1923]. The correction accounts for time dilation, i.e. moving clocks beat slower than clocks at rest. A standard example is as follows [Ashby and Spilker, 1996]. Consider a train moving at velocity v along the x axis. A light pulse is emitted from one side of the train and reflects against a mirror hung on the opposite wall. The light pulse is then received and the round trip time recorded. If the train car has width w (see Fig. 7.1), then the round trip time according to an observer on the train is: 110 Mirror w Light Pulse Emit/Receive Light Pulse Experiment as Observed on Board the Train Mirror (at time of reflection) v w Emit Pulse Receive Pulse Light Pulse Experiment as Viewed by a Stationary Observer Figure 7.1 Illustration of Time Dilation Using Light Pulses 111 2w t ' (7.1) train c where c is the speed of light.
    [Show full text]
  • Time and Frequency Users' Manual
    ,>'.)*• r>rJfl HKra mitt* >\ « i If I * I IT I . Ip I * .aference nbs Publi- cations / % ^m \ NBS TECHNICAL NOTE 695 U.S. DEPARTMENT OF COMMERCE/National Bureau of Standards Time and Frequency Users' Manual 100 .U5753 No. 695 1977 NATIONAL BUREAU OF STANDARDS 1 The National Bureau of Standards was established by an act of Congress March 3, 1901. The Bureau's overall goal is to strengthen and advance the Nation's science and technology and facilitate their effective application for public benefit To this end, the Bureau conducts research and provides: (1) a basis for the Nation's physical measurement system, (2) scientific and technological services for industry and government, a technical (3) basis for equity in trade, and (4) technical services to pro- mote public safety. The Bureau consists of the Institute for Basic Standards, the Institute for Materials Research the Institute for Applied Technology, the Institute for Computer Sciences and Technology, the Office for Information Programs, and the Office of Experimental Technology Incentives Program. THE INSTITUTE FOR BASIC STANDARDS provides the central basis within the United States of a complete and consist- ent system of physical measurement; coordinates that system with measurement systems of other nations; and furnishes essen- tial services leading to accurate and uniform physical measurements throughout the Nation's scientific community, industry, and commerce. The Institute consists of the Office of Measurement Services, and the following center and divisions: Applied Mathematics
    [Show full text]
  • The Impact of the Speed of Light on Financial Markets and Their Regulation
    When Finance Meets Physics: The Impact of the Speed of Light on Financial Markets and their Regulation by James J. Angel, Ph.D., CFA Associate Professor of Finance McDonough School of Business Georgetown University 509 Hariri Building Washington DC 20057 USA 1.202.687.3765 [email protected] The Financial Review, Forthcoming, May 2014 · Volume 49 · No. 2 Abstract: Modern physics has demonstrated that matter behaves very differently as it approaches the speed of light. This paper explores the implications of modern physics to the operation and regulation of financial markets. Information cannot move faster than the speed of light. The geographic separation of market centers means that relativistic considerations need to be taken into account in the regulation of markets. Observers in different locations may simultaneously observe different “best” prices. Regulators may not be able to determine which transactions occurred first, leading to problems with best execution and trade- through rules. Catastrophic software glitches can quantum tunnel through seemingly impregnable quality control procedures. Keywords: Relativity, Financial Markets, Regulation, High frequency trading, Latency, Best execution JEL Classification: G180 The author is also on the board of directors of the Direct Edge stock exchanges (EDGX and EDGA). I wish to thank the editor and referee for extremely helpful comments and suggestions. I also wish to thank the U.K. Foresight Project, for providing financial support for an earlier version of this paper. All opinions are strictly my own and do not necessarily represent those of Georgetown University, Direct Edge, the U.K. Foresight Project, The Financial Review, or anyone else for that matter.
    [Show full text]
  • Using Microsecond Single-Molecule FRET to Determine the Assembly
    Using microsecond single-molecule FRET to determine PNAS PLUS the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks Carey Phelpsa,b,1, Brett Israelsa,b, Davis Josea, Morgan C. Marsha,b, Peter H. von Hippela,2, and Andrew H. Marcusa,b,2 aDepartment of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403; and bDepartment of Chemistry and Biochemistry, Oregon Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403 Edited by Stephen C. Kowalczykowski, University of California, Davis, CA, and approved March 20, 2017 (received for review December 2, 2016) DNA replication is a core biological process that occurs in pro- complete coverage of the exposed ssDNA templates at the precisely karyotic cells at high speeds (∼1 nucleotide residue added per regulated concentration of protein that needs to be maintained in millisecond) and with high fidelity (fewer than one misincorpora- the infected Escherichia coli cell (8, 9). The gp32 protein has an tion event per 107 nucleotide additions). The ssDNA binding pro- N-terminal domain, a C-terminal domain, and a core domain. tein [gene product 32 (gp32)] of the T4 bacteriophage is a central The N-terminal domain is necessary for the cooperative binding integrating component of the replication complex that must con- of the gp32 protein through its interactions with the core domain of tinuously bind to and unbind from transiently exposed template an adjacent gp32 protein. To bind to ssDNA, the C-terminal domain strands during DNA synthesis. We here report microsecond single- of the gp32 protein must undergo a conformational change that molecule FRET (smFRET) measurements on Cy3/Cy5-labeled primer- exposes the positively charged region of its core domain, which in template (p/t) DNA constructs in the presence of gp32.
    [Show full text]
  • Aquatic Primary Productivity Field Protocols for Satellite Validation and Model Synthesis (DRAFT)
    Ocean Optics & Biogeochemistry Protocols for Satellite Ocean Colour Sensor Validation IOCCG Protocol Series Volume 7.0, 2021 Aquatic Primary Productivity Field Protocols for Satellite Validation and Model Synthesis (DRAFT) Report of a NASA-sponsored workshop with contributions (alphabetical) from: William M. Balch Bigelow Laboratory for Ocean Sciences, Maine, USA Magdalena M. Carranza Monterey Bay Aquarium Research Institute, California, USA Ivona Cetinic University Space Research Association, NASA Goddard Space Flight Center, Maryland, USA Joaquín E. Chaves Science Systems and Applications, Inc., NASA Goddard Space Flight Center, Maryland, USA Solange Duhamel University of Arizona, Arizona, USA Zachary K. Erickson University Space Research Association, NASA Goddard Space Flight Center, Maryland, USA Andrea J. Fassbender NOAA Pacific Marine Environmental Laboratory, Washington, USA Ana Fernández-Carrera Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany Sara Ferrón University of Hawaii at Manoa, Hawaii, USA E. Elena García-Martín National Oceanography Centre, Southampton, UK Joaquim Goes Lamont Doherty Earth Observatory at Columbia University, New York, USA Helga do Rosario Gomes Lamont Doherty Earth Observatory at Columbia University, New York, USA Maxim Y. Gorbunov Department of Marine and Coastal Sciences, Rutgers University, New Jersey, USA Kjell Gundersen Plankton Research Group, Institute of Marine Research, Bergen, Norway Kimberly Halsey Department of Microbiology, Oregon State University, Oregon, USA Toru Hirawake
    [Show full text]
  • Nanosecond X-Ray Photon Correlation Spectroscopy Using Pulse Time
    research papers Nanosecond X-ray photon correlation spectroscopy IUCrJ using pulse time structure of a storage-ring source ISSN 2052-2525 NEUTRONjSYNCHROTRON Wonhyuk Jo,a Fabian Westermeier,a Rustam Rysov,a Olaf Leupold,a Florian Schulz,b,c Steffen Tober,b‡ Verena Markmann,a Michael Sprung,a Allesandro Ricci,a Torsten Laurus,a Allahgholi Aschkan,a Alexander Klyuev,a Ulrich Trunk,a Heinz Graafsma,a Gerhard Gru¨bela,c and Wojciech Rosekera* Received 25 September 2020 Accepted 2 December 2020 aDeutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany, bInstitute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany, and cThe Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany. *Correspondence e-mail: [email protected] Edited by Dr T. Ishikawa, Coherent X-ray Optics Laboratory, Harima Institute, RIKEN, Japan X-ray photon correlation spectroscopy (XPCS) is a routine technique to study slow dynamics in complex systems at storage-ring sources. Achieving ‡ Current address: Deutsches Elektronen- Synchrotron (DESY), Notkestr. 85, 22607 nanosecond time resolution with the conventional XPCS technique is, however, Hamburg, Germany. still an experimentally challenging task requiring fast detectors and sufficient photon flux. Here, the result of a nanosecond XPCS study of fast colloidal Keywords: materials science; nanoscience; dynamics is shown by employing an adaptive gain integrating pixel detector SAXS; dynamical studies; time-resolved studies; (AGIPD) operated at frame rates of the intrinsic pulse structure of the storage X-ray photon correlation spectroscopy; adaptive ring. Correlation functions from single-pulse speckle patterns with the shortest gain integrating pixel detectors; storage rings; pulse structures.
    [Show full text]
  • Lecture 12: March 18 12.1 Overview 12.2 Clock Synchronization
    CMPSCI 677 Operating Systems Spring 2019 Lecture 12: March 18 Lecturer: Prashant Shenoy Scribe: Jaskaran Singh, Abhiram Eswaran(2018) Announcements: Midterm Exam on Friday Mar 22, Lab 2 will be released today, it is due after the exam. 12.1 Overview The topic of the lecture is \Time ordering and clock synchronization". This lecture covered the following topics. Clock Synchronization : Motivation, Cristians algorithm, Berkeley algorithm, NTP, GPS Logical Clocks : Event Ordering 12.2 Clock Synchronization 12.2.1 The motivation of clock synchronization In centralized systems and applications, it is not necessary to synchronize clocks since all entities use the system clock of one machine for time-keeping and one can determine the order of events take place according to their local timestamps. However, in a distributed system, lack of clock synchronization may cause issues. It is because each machine has its own system clock, and one clock may run faster than the other. Thus, one cannot determine whether event A in one machine occurs before event B in another machine only according to their local timestamps. For example, you modify files and save them on machine A, and use another machine B to compile the files modified. If one wishes to compile files in order and B has a faster clock than A, you may not correctly compile the files because the time of compiling files on B may be later than the time of editing files on A and we have nothing but local timestamps on different machines to go by, thus leading to errors. 12.2.2 How physical clocks and time work 1) Use astronomical metrics (solar day) to tell time: Solar noon is the time that sun is directly overhead.
    [Show full text]
  • Low Latency – How Low Can You Go?
    WHITE PAPER Low Latency – How Low Can You Go? Low latency has always been an important consideration in telecom networks for voice, video, and data, but recent changes in applications within many industry sectors have brought low latency right to the forefront of the industry. The finance industry and algorithmic trading in particular, or algo-trading as it is known, is a commonly quoted example. Here latency is critical, and to quote Information Week magazine, “A 1-millisecond advantage in trading applications can be worth $100 million a year to a major brokerage firm.” This drives a huge focus on all aspects of latency, including the communications systems between the brokerage firm and the exchange. However, while the finance industry is spending a lot of money on low- latency services between key locations such as New York and Chicago or London and Frankfurt, this is actually only a small part of the wider telecom industry. Many other industries are also now driving lower and lower latency in their networks, such as for cloud computing and video services. Also, as mobile operators start to roll out 5G services, latency in the xHaul mobile transport network, especially the demanding fronthaul domain, becomes more and more important in order to reach the stringent 5G requirements required for the new class of ultra-reliable low-latency services. This white paper will address the drivers behind the recent rush to low- latency solutions and networks and will consider how network operators can remove as much latency as possible from their networks as they also race to zero latency.
    [Show full text]
  • Clock Synchronization Clock Synchronization Part 2, Chapter 5
    Clock Synchronization Clock Synchronization Part 2, Chapter 5 Roger Wattenhofer ETH Zurich – Distributed Computing – www.disco.ethz.ch 5/1 5/2 Overview TexPoint fonts used in EMF. Motivation Read the TexPoint manual before you delete this box.: AAAA A • Logical Time (“happened-before”) • Motivation • Determine the order of events in a distributed system • Real World Clock Sources, Hardware and Applications • Synchronize resources • Clock Synchronization in Distributed Systems • Theory of Clock Synchronization • Physical Time • Protocol: PulseSync • Timestamp events (email, sensor data, file access times etc.) • Synchronize audio and video streams • Measure signal propagation delays (Localization) • Wireless (TDMA, duty cycling) • Digital control systems (ESP, airplane autopilot etc.) 5/3 5/4 Properties of Clock Synchronization Algorithms World Time (UTC) • External vs. internal synchronization • Atomic Clock – External sync: Nodes synchronize with an external clock source (UTC) – UTC: Coordinated Universal Time – Internal sync: Nodes synchronize to a common time – SI definition 1s := 9192631770 oscillation cycles of the caesium-133 atom – to a leader, to an averaged time, ... – Clocks excite these atoms to oscillate and count the cycles – Almost no drift (about 1s in 10 Million years) • One-shot vs. continuous synchronization – Getting smaller and more energy efficient! – Periodic synchronization required to compensate clock drift • Online vs. offline time information – Offline: Can reconstruct time of an event when needed • Global vs.
    [Show full text]
  • Simulating Nucleic Acids from Nanoseconds to Microseconds
    UC Irvine UC Irvine Electronic Theses and Dissertations Title Simulating Nucleic Acids from Nanoseconds to Microseconds Permalink https://escholarship.org/uc/item/6cj4n691 Author Bascom, Gavin Dennis Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, IRVINE Simulating Nucleic Acids from Nanoseconds to Microseconds DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry, with a specialization in Theoretical Chemistry by Gavin Dennis Bascom Dissertation Committee: Professor Ioan Andricioaei, Chair Professor Douglas Tobias Professor Craig Martens 2014 Appendix A c 2012 American Chemical Society All other materials c 2014 Gavin Dennis Bascom DEDICATION To my parents, my siblings, and to my love, Lauren. ii TABLE OF CONTENTS Page LIST OF FIGURES vi LIST OF TABLES x ACKNOWLEDGMENTS xi CURRICULUM VITAE xii ABSTRACT OF THE DISSERTATION xiv 1 Introduction 1 1.1 Nucleic Acids in a Larger Context . 1 1.2 Nucleic Acid Structure . 5 1.2.1 DNA Structure/Motion Basics . 5 1.2.2 RNA Structure/Motion Basics . 8 1.2.3 Experimental Techniques for Nucleic Acid Structure Elucidation . 9 1.3 Simulating Trajectories by Molecular Dynamics . 11 1.3.1 Integrating Newtonian Equations of Motion and Force Fields . 12 1.3.2 Treating Non-bonded Interactions . 15 1.4 Defining Our Scope . 16 2 The Nanosecond 28 2.1 Introduction . 28 2.1.1 Biological Processes of Nucleic Acids at the Nanosecond Timescale . 29 2.1.2 DNA Motions on the Nanosecond Timescale . 32 2.1.3 RNA Motions on the Nanosecond Timescale .
    [Show full text]
  • Microsecond and Millisecond Dynamics in the Photosynthetic
    Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy Toru Kondoa,1,2, Jesse B. Gordona, Alberta Pinnolab,c, Luca Dall’Ostob, Roberto Bassib, and Gabriela S. Schlau-Cohena,1 aDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Biotechnology, University of Verona, 37134 Verona, Italy; and cDepartment of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy Edited by Catherine J. Murphy, University of Illinois at Urbana–Champaign, Urbana, IL, and approved April 11, 2019 (received for review December 13, 2018) Biological systems are subjected to continuous environmental (5–9) or intensity correlation function analysis (10). CPF analysis fluctuations, and therefore, flexibility in the structure and func- bins the photon data, obscuring fast dynamics. In contrast, inten- tion of their protein building blocks is essential for survival. sity correlation function analysis characterizes fluctuations in the Protein dynamics are often local conformational changes, which photon arrival rate, accessing dynamics down to microseconds. allows multiple dynamical processes to occur simultaneously and However, the fluorescence lifetime is a powerful indicator of rapidly in individual proteins. Experiments often average over conformation for chromoproteins and for lifetime-based FRET these dynamics and their multiplicity, preventing identification measurements, yet it is ignored in intensity-based analyses. of the molecular origin and impact on biological function. Green 2D fluorescence lifetime correlation (2D-FLC) analysis was plants survive under high light by quenching excess energy, recently introduced as a method to both resolve fast dynam- and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the ics and use fluorescence lifetime information (11, 12).
    [Show full text]